[petsc-users] Problem with fortran version of ex29 in ksp
Barry Smith
bsmith at mcs.anl.gov
Thu Apr 26 18:22:35 CDT 2012
From the manual page for MatSetValuesStencil():
MatSetValuesStencil() uses 0-based row and column numbers in Fortran
as well as in C.
On Apr 26, 2012, at 5:21 PM, TAY wee-beng wrote:
> Hi,
>
> I managed to remove the out of range error by removing
>
> num = num + 1 from
>
> col(MatStencil_i,num) = i
>
> col(MatStencil_j,num) = j+1
>
> num = num + 1
>
> call MatSetValuesStencil(jac,i1,row,num,col,v,INSERT_VALUES,ierr)
>
> In C, num will give the number 5 since num start from 0.
>
> In fortran, num starts from 1 so num = num + 1 before MatSetValuesStencil must be removed.
>
> I still can't get the same ans. I will try to figure it out. Just to confirm, this subroutine:
>
> call MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr)
>
> is not added in fortran, although it is used in C.
> Yours sincerely,
>
> TAY wee-beng
>
>
> On 26/4/2012 9:29 PM, Matthew Knepley wrote:
>> On Thu, Apr 26, 2012 at 3:26 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>> Hi,
>>
>> Thanks for pointing out my mistake. I'm still learning about the code. I corrected but I still get the error:
>>
>> I am sure its another simple bug. Go in with the debugger. When it says you are inserting a new nonzero,
>> back up the stack to your routine and see what indices you are tying to insert. If its not part of the stencil,
>> you have found the bug.
>>
>> Matt
>>
>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>> --------
>> [0]PETSC ERROR: Argument out of range!
>> [0]PETSC ERROR: New nonzero at (2,4) caused a malloc!
>> [0]PETSC ERROR: ----------------------------------------------------------------
>>
>> boundary condition region:
>>
>> num = 1
>>
>> if (j/=0) then
>>
>> v(num) = -rho*HxdHy
>>
>> col(MatStencil_i,num) = i
>>
>> col(MatStencil_j,num) = j-1
>>
>> num = num + 1
>>
>> end if
>>
>> if (i/=0) then
>>
>> v(num) = -rho*HydHx
>>
>> col(MatStencil_i,num) = i-1
>>
>> col(MatStencil_j,num) = j
>>
>> num = num + 1
>>
>> end if
>>
>> if (i/=mx-1) then
>>
>> v(num) = -rho*HydHx
>>
>> col(MatStencil_i,num) = i+1
>>
>> col(MatStencil_j,num) = j
>>
>> num = num + 1
>>
>> end if
>>
>> if (j/=my-1) then
>>
>> v(num) = -rho*HxdHy
>>
>> col(MatStencil_i,num) = i
>>
>> col(MatStencil_j,num) = j+1
>>
>> num = num + 1
>>
>> end if
>>
>> v(num) = (num/2.0)*rho*(HxdHy + HydHx)
>>
>> col(MatStencil_i,num) = i
>>
>> col(MatStencil_j,num) = j+1
>>
>> num = num + 1
>>
>> call MatSetValuesStencil(jac,i1,row,num,col,v,INSERT_VALUES,ierr)
>> Yours sincerely,
>>
>> TAY wee-beng
>>
>>
>> On 26/4/2012 2:45 PM, Matthew Knepley wrote:
>>> On Thu, Apr 26, 2012 at 8:27 AM, TAY wee-beng <zonexo at gmail.com> wrote:
>>> Hi,
>>>
>>> Is there an answer to the question below?
>>> I still can't get it working.
>>>
>>> Thanks.
>>>
>>>
>>> Hi,
>>>
>>> There's no error now but I didn't get the same ans as ex29. I believe the error lies in the boundary evaluation of v.
>>>
>>> In c, the code is :
>>>
>>> else if (user->bcType == NEUMANN) {
>>> num = 0;
>>> if (j!=0) {
>>> v[num] = -rho*HxdHy; col[num].i = i; col[num].j = j-1;
>>> ^^^ See this?
>>> num++;
>>> }
>>> if (i!=0) {
>>> v[num] = -rho*HydHx; col[num].i = i-1; col[num].j = j;
>>> num++;
>>> }
>>> if (i!=mx-1) {
>>> v[num] = -rho*HydHx; col[num].i = i+1; col[num].j = j;
>>> num++;
>>> }
>>> if (j!=my-1) {
>>> v[num] = -rho*HxdHy; col[num].i = i; col[num].j = j+1;
>>> num++;
>>> }
>>> v[num] = (num/2.0)*rho*(HxdHy + HydHx); col[num].i = i; col[num].j = j;
>>> num++;
>>> ierr = MatSetValuesStencil(jac,1,&row,num,col,v,INSERT_VALUES);CHKERRQ(ierr);
>>>
>>> In fortran, I have changed to :
>>>
>>> else if (bc_cond == 2) then
>>>
>>> num = 1
>>>
>>> if (j/=0) then
>>>
>>> v(num) = -rho*HxdHy
>>>
>>> col(MatStencil_i,1) = i
>>> ^^ Why is this 1 in stead of 'num'?
>>>
>>> Matt
>>>
>>>
>>> col(MatStencil_j,2) = j-1
>>>
>>> num = num + 1
>>>
>>> end if
>>>
>>> if (i/=0) then
>>>
>>> v(num) = -rho*HydHx
>>>
>>> col(MatStencil_i,1) = i-1
>>>
>>> col(MatStencil_j,2) = j
>>>
>>> num = num + 1
>>>
>>> end if
>>>
>>> if (i/=mx-1) then
>>>
>>> v(num) = -rho*HydHx
>>>
>>> col(MatStencil_i,1) = i+1
>>>
>>> col(MatStencil_j,2) = j
>>>
>>> num = num + 1
>>>
>>> end if
>>>
>>> if (j/=my-1) then
>>>
>>> v(num) = -rho*HxdHy
>>>
>>> col(MatStencil_i,1) = i
>>>
>>> col(MatStencil_j,2) = j+1
>>>
>>> num = num + 1
>>>
>>> end if
>>>
>>> v(num) = (num/2.0)*rho*(HxdHy + HydHx)
>>>
>>> col(MatStencil_i,1) = i
>>>
>>> col(MatStencil_j,2) = j+1
>>>
>>> num = num + 1
>>>
>>> call MatSetValuesStencil(jac,i1,row,num,col,v,INSERT_VALUES,ierr)
>>>
>>> However, I got the error:
>>>
>>> [0]PETSC ERROR: --------------------- Error Message ---------------------------
>>> --------
>>> [0]PETSC ERROR: Argument out of range!
>>> [0]PETSC ERROR: New nonzero at (1,3) caused a malloc!
>>> [0]PETSC ERROR: ---------------------------------------------------------------
>>>
>>> How such is be defined in Fortran?
>>>
>>> Thank you
>>> Yours sincerely,
>>>
>>> TAY wee-beng
>>>
>>>
>>> On 25/4/2012 12:06 AM, Matthew Knepley wrote:
>>>> On Tue, Apr 24, 2012 at 4:57 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>>> Hi,
>>>>
>>>> I still got the same error the moment this subroutine is called, after changing to :
>>>>
>>>> call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,PETSC_NULL_INTEGER,PETSC_NULL_OBJECT,nullspace,ierr)
>>>>
>>>> Argument 3 should be 0.
>>>>
>>>> Matt
>>>>
>>>> [0]PETSC ERROR: Null argument, when expecting valid pointer!
>>>> [0]PETSC ERROR: Null Object: Parameter # 4!
>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>> --------
>>>> [0]PETSC ERROR: Petsc Development HG revision: fc934c1d84bc6ba8e2686702a8a99539d
>>>> 50af122 HG Date: Mon Apr 23 11:39:32 2012 -0500
>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>> --------
>>>> [0]PETSC ERROR: c:\obj_tmp\ex29f\Debug\ex29f.exe on a petsc-3.2 named USER-PC by
>>>> User Tue Apr 24 22:54:50 2012
>>>> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008
>>>> /lib
>>>> [0]PETSC ERROR: Configure run at Mon Apr 23 21:45:20 2012
>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc="win32fe ifor
>>>> t" --with-cxx="win32fe cl" --with-mpi-dir=/cygdrive/d/Lib/MPICH2/ --download-f-b
>>>> las-lapack=1 --prefix=/cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008 --with-debuggin
>>>> g=1 --useThreads=0
>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>> --------
>>>> [0]PETSC ERROR: MatNullSpaceCreate() line 250 in src/mat/interface/C:\temp\PETSC
>>>> -~1\src\mat\INTERF~1\matnull.c
>>>> Yours sincerely,
>>>>
>>>> TAY wee-beng
>>>>
>>>>
>>>> On 24/4/2012 10:37 PM, Matthew Knepley wrote:
>>>>> On Tue, Apr 24, 2012 at 4:32 PM, TAY wee-beng <zonexo at gmail.com> wrote:
>>>>> Hi,
>>>>>
>>>>> I'm trying to rewrite ex29 (KSP^Laplacian, 2d) from c to fortran version. The fortran version is based on the template of ex22f, which is in 3d.
>>>>>
>>>>> I have attached the code below. I have 2 problems.
>>>>>
>>>>> 1. When i3 = -3, in dirichlet BC, I got the same answer as ex29 in c version.
>>>>>
>>>>> However, when I change i3 to -4, I got the following error:
>>>>>
>>>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Argument out of range!
>>>>> [0]PETSC ERROR: New nonzero at (9,1) caused a malloc!
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Petsc Development HG revision: fc934c1d84bc6ba8e2686702a8a99539d
>>>>> 50af122 HG Date: Mon Apr 23 11:39:32 2012 -0500
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: c:\obj_tmp\ex29f\Debug\ex29f.exe on a petsc-3.2 named USER-PC by
>>>>> User Tue Apr 24 22:08:46 2012
>>>>> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008
>>>>> /lib
>>>>> [0]PETSC ERROR: Configure run at Mon Apr 23 21:45:20 2012
>>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc="win32fe ifor
>>>>> t" --with-cxx="win32fe cl" --with-mpi-dir=/cygdrive/d/Lib/MPICH2/ --download-f-b
>>>>> las-lapack=1 --prefix=/cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008 --with-debuggin
>>>>> g=1 --useThreads=0
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: MatSetValues_SeqAIJ() line 331 in src/mat/impls/aij/seq/C:\temp\
>>>>> PETSC-~1\src\mat\impls\aij\seq\aij.c
>>>>> [0]PETSC ERROR: MatSetValues() line 1148 in src/mat/interface/C:\temp\PETSC-~1\s
>>>>> rc\mat\INTERF~1\matrix.c
>>>>> [0]PETSC ERROR: MatSetValuesLocal() line 2003 in src/mat/interface/C:\temp\PETSC
>>>>> -~1\src\mat\INTERF~1\matrix.c
>>>>> [0]PETSC ERROR: MatSetValuesStencil() line 1379 in src/mat/interface/C:\temp\PET
>>>>> SC-~1\src\mat\INTERF~1\matrix.c
>>>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Argument out of range!
>>>>> [0]PETSC ERROR: New nonzero at (10,2) caused a malloc!
>>>>>
>>>>> ...
>>>>>
>>>>> What did I do wrong?
>>>>>
>>>>>
>>>>> 2. When I wanted to use the neumann BC, following ex29, I added :
>>>>>
>>>>> In subroutine ComputeRHS
>>>>>
>>>>> call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,nullspace,ierr)
>>>>>
>>>>> call MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr)
>>>>>
>>>>> call MatNullSpaceDestroy(nullspace,ierr)
>>>>>
>>>>> and in subroutine ComputeMatrix
>>>>>
>>>>> call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,nullspace,ierr)
>>>>>
>>>>> call MatSetNullSpace(jac,nullspace,ierr)
>>>>>
>>>>> call MatNullSpaceDestroy(nullspace,ierr)
>>>>>
>>>>> When I compile, it says unresolved external symbol MatNullSpaceRemove. Removing MatNullSpaceRemove, I can compile but running gives the error:
>>>>>
>>>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Corrupt argument:
>>>>> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
>>>>> [0]PETSC ERROR: Invalid Pointer to Object: Parameter # 4!
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Petsc Development HG revision: fc934c1d84bc6ba8e2686702a8a99539d
>>>>> 50af122 HG Date: Mon Apr 23 11:39:32 2012 -0500
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: c:\obj_tmp\ex29f\Debug\ex29f.exe on a petsc-3.2 named USER-PC by
>>>>> User Tue Apr 24 22:30:31 2012
>>>>> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008
>>>>> /lib
>>>>> [0]PETSC ERROR: Configure run at Mon Apr 23 21:45:20 2012
>>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc="win32fe ifor
>>>>> t" --with-cxx="win32fe cl" --with-mpi-dir=/cygdrive/d/Lib/MPICH2/ --download-f-b
>>>>> las-lapack=1 --prefix=/cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008 --with-debuggin
>>>>> g=1 --useThreads=0
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: MatNullSpaceCreate() line 250 in src/mat/interface/C:\temp\PETSC
>>>>> -~1\src\mat\INTERF~1\matnull.c
>>>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Invalid argument!
>>>>> [0]PETSC ERROR: Wrong type of object: Parameter # 1!
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Petsc Development HG revision: fc934c1d84bc6ba8e2686702a8a99539d
>>>>> 50af122 HG Date: Mon Apr 23 11:39:32 2012 -0500
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: c:\obj_tmp\ex29f\Debug\ex29f.exe on a petsc-3.2 named USER-PC by
>>>>> User Tue Apr 24 22:30:31 2012
>>>>> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008
>>>>> /lib
>>>>> [0]PETSC ERROR: Configure run at Mon Apr 23 21:45:20 2012
>>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc="win32fe ifor
>>>>> t" --with-cxx="win32fe cl" --with-mpi-dir=/cygdrive/d/Lib/MPICH2/ --download-f-b
>>>>> las-lapack=1 --prefix=/cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008 --with-debuggin
>>>>> g=1 --useThreads=0
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: MatNullSpaceDestroy() line 305 in src/mat/interface/C:\temp\PETS
>>>>> C-~1\src\mat\INTERF~1\matnull.c
>>>>> [0]PETSC ERROR: ourdmfunction() line 30 in src/dm/interface/ftn-custom/C:\temp\P
>>>>> ETSC-~1\src\dm\INTERF~1\FTN-CU~1\zdmf.c
>>>>> [0]PETSC ERROR: DMComputeFunction() line 1783 in src/dm/interface/C:\temp\PETSC-
>>>>> ~1\src\dm\INTERF~1\dm.c
>>>>> [0]PETSC ERROR: KSPSetUp() line 218 in src/ksp/ksp/interface/C:\temp\PETSC-~1\sr
>>>>> c\ksp\ksp\INTERF~1\itfunc.c
>>>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Corrupt argument:
>>>>> see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind!
>>>>> [0]PETSC ERROR: Invalid Pointer to Object: Parameter # 4!
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Petsc Development HG revision: fc934c1d84bc6ba8e2686702a8a99539d
>>>>> 50af122 HG Date: Mon Apr 23 11:39:32 2012 -0500
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: c:\obj_tmp\ex29f\Debug\ex29f.exe on a petsc-3.2 named USER-PC by
>>>>> User Tue Apr 24 22:30:31 2012
>>>>> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008
>>>>> /lib
>>>>> [0]PETSC ERROR: Configure run at Mon Apr 23 21:45:20 2012
>>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc="win32fe ifor
>>>>> t" --with-cxx="win32fe cl" --with-mpi-dir=/cygdrive/d/Lib/MPICH2/ --download-f-b
>>>>> las-lapack=1 --prefix=/cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008 --with-debuggin
>>>>> g=1 --useThreads=0
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: MatNullSpaceCreate() line 250 in src/mat/interface/C:\temp\PETSC
>>>>> -~1\src\mat\INTERF~1\matnull.c
>>>>> [0]PETSC ERROR: --------------------- Error Message ----------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Invalid argument!
>>>>> [0]PETSC ERROR: Wrong type of object: Parameter # 1!
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: Petsc Development HG revision: fc934c1d84bc6ba8e2686702a8a99539d
>>>>> 50af122 HG Date: Mon Apr 23 11:39:32 2012 -0500
>>>>> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
>>>>> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>>>> [0]PETSC ERROR: See docs/index.html for manual pages.
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: c:\obj_tmp\ex29f\Debug\ex29f.exe on a petsc-3.2 named USER-PC by
>>>>> User Tue Apr 24 22:30:31 2012
>>>>> [0]PETSC ERROR: Libraries linked from /cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008
>>>>> /lib
>>>>> [0]PETSC ERROR: Configure run at Mon Apr 23 21:45:20 2012
>>>>> [0]PETSC ERROR: Configure options --with-cc="win32fe cl" --with-fc="win32fe ifor
>>>>> t" --with-cxx="win32fe cl" --with-mpi-dir=/cygdrive/d/Lib/MPICH2/ --download-f-b
>>>>> las-lapack=1 --prefix=/cygdrive/d/Lib/petsc-3.2-dev_win32_vs2008 --with-debuggin
>>>>> g=1 --useThreads=0
>>>>> [0]PETSC ERROR: ----------------------------------------------------------------
>>>>> --------
>>>>> [0]PETSC ERROR: MatNullSpaceDestroy() line 305 in src/mat/interface/C:\temp\PETS
>>>>> C-~1\src\mat\INTERF~1\matnull.c
>>>>> [0]PETSC ERROR: ourdmfunction() line 30 in src/dm/interface/ftn-custom/C:\temp\P
>>>>> ETSC-~1\src\dm\INTERF~1\FTN-CU~1\zdmf.c
>>>>> [0]PETSC ERROR: DMComputeFunction() line 1783 in src/dm/interface/C:\temp\PETSC-
>>>>> ~1\src\dm\INTERF~1\dm.c
>>>>> [0]PETSC ERROR: KSPSetUp() line 218 in src/ksp/ksp/interface/C:\temp\PETSC-~1\sr
>>>>> c\ksp\ksp\INTERF~1\itfunc.c
>>>>> [0]PETSC ERROR: KSPSolve() line 402 in src/ksp/ksp/interface/C:\temp\PETSC-~1\sr
>>>>> c\ksp\ksp\INTERF~1\itfunc.c
>>>>> Vector Object:Vec_0000000084000000_0 1 MPI processes
>>>>> type: mpi
>>>>> Process [0]
>>>>>
>>>>> What's wrong?
>>>>>
>>>>>
>>>>> program ex29f
>>>>>
>>>>> implicit none
>>>>>
>>>>> ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>>> ! Include files
>>>>> ! - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
>>>>> !
>>>>> ! petscsys.h - base PETSc routines petscvec.h - vectors
>>>>> ! petscmat.h - matrices
>>>>> ! petscksp.h - Krylov subspace methods petscpc.h - preconditioners
>>>>>
>>>>> #include "finclude/petsc.h90"
>>>>>
>>>>> PetscErrorCode ierr
>>>>>
>>>>> DM da
>>>>>
>>>>> KSP ksp
>>>>>
>>>>> Vec x
>>>>>
>>>>> external ComputeRHS,ComputeMatrix
>>>>>
>>>>> PetscInt i1,i3
>>>>>
>>>>> call PetscInitialize(PETSC_NULL_CHARACTER,ierr)
>>>>>
>>>>> i3 = -4
>>>>>
>>>>> i1 = 1
>>>>>
>>>>> call KSPCreate(MPI_COMM_WORLD,ksp,ierr)
>>>>>
>>>>> call DMDACreate2d(PETSC_COMM_WORLD,DMDA_BOUNDARY_NONE,DMDA_BOUNDARY_NONE,DMDA_STENCIL_STAR,i3,i3,PETSC_DECIDE,PETSC_DECIDE,i1,i1,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,da,ierr)
>>>>> call DMSetFunction(da,ComputeRHS,ierr)
>>>>> call DMSetJacobian(da,ComputeMatrix,ierr)
>>>>> call KSPSetDM(ksp,da,ierr)
>>>>>
>>>>> call KSPSetFromOptions(ksp,ierr)
>>>>> call KSPSetUp(ksp,ierr)
>>>>> call KSPSolve(ksp,PETSC_NULL_OBJECT,PETSC_NULL_OBJECT,ierr)
>>>>> call KSPGetSolution(ksp,x,ierr)
>>>>> call VecView(x,PETSC_VIEWER_STDOUT_WORLD,ierr)
>>>>> call KSPDestroy(ksp,ierr)
>>>>> call DMDestroy(da,ierr)
>>>>> call PetscFinalize(ierr)
>>>>>
>>>>> end program ex29f
>>>>>
>>>>> subroutine ComputeRHS(da,x,b,ierr)
>>>>>
>>>>> implicit none
>>>>>
>>>>> #include "finclude/petsc.h90"
>>>>>
>>>>> PetscErrorCode ierr
>>>>> PetscInt i,j,mx,my,xm,ym,xs,ys
>>>>> PetscScalar h,nu,rho
>>>>> PetscScalar Hx,Hy
>>>>> PetscScalar,pointer :: array(:,:)
>>>>> Vec x,b
>>>>> DM da
>>>>> MatNullSpace nullspace !>neumann BC
>>>>>
>>>>> nu = 0.1
>>>>>
>>>>> call DMDAGetInfo(da,PETSC_NULL_INTEGER,mx,my,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr)
>>>>>
>>>>> Hx = 1.d0 / (mx-1)
>>>>>
>>>>> Hy = 1.d0 / (my-1)
>>>>>
>>>>> call DMDAGetCorners(da,xs,ys,PETSC_NULL_INTEGER,xm,ym,PETSC_NULL_INTEGER,ierr)
>>>>>
>>>>> call DMDAVecGetArrayF90(da,b,array,ierr)
>>>>>
>>>>> do j = ys,ys+ym-1
>>>>>
>>>>> do i = xs,xs+xm-1
>>>>>
>>>>> array(i,j) = exp(-(i*Hx)*(i*Hx)/nu)*exp(-(j*Hy)*(j*Hy)/nu)*Hx*Hy
>>>>>
>>>>> end do
>>>>>
>>>>> end do
>>>>>
>>>>> call DMDAVecRestoreArrayF90(da,b,array,ierr)
>>>>>
>>>>> call VecAssemblyBegin(b,ierr)
>>>>>
>>>>> call VecAssemblyEnd(b,ierr)
>>>>>
>>>>> !call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,nullspace,ierr)
>>>>>
>>>>> 4th argument should be PETSC_NULL_OBJECT.
>>>>>
>>>>> Matt
>>>>>
>>>>> !call MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr)
>>>>>
>>>>> !call MatNullSpaceDestroy(nullspace,ierr)
>>>>>
>>>>> end subroutine ComputeRHS
>>>>>
>>>>>
>>>>> subroutine ComputeMatrix(da,x,JJ,jac,str,ierr)
>>>>>
>>>>> implicit none
>>>>>
>>>>> #include "finclude/petsc.h90"
>>>>>
>>>>> Mat jac,JJ
>>>>>
>>>>> PetscErrorCode ierr
>>>>>
>>>>> DM da
>>>>>
>>>>> PetscInt i,j,k,mx,my,xm
>>>>>
>>>>> PetscInt ym,xs,ys,i1,i5
>>>>>
>>>>> PetscScalar v(5),Hx,Hy,rho,centerRho
>>>>>
>>>>> PetscScalar HydHx
>>>>>
>>>>> PetscScalar HxdHy
>>>>>
>>>>> MatStencil row(4),col(4,5)
>>>>>
>>>>> Vec x
>>>>>
>>>>> MatStructure str
>>>>>
>>>>> MatNullSpace nullspace !>neumann BC
>>>>>
>>>>> rho = 1.0
>>>>>
>>>>> i1 = 1
>>>>>
>>>>> i5 = 5
>>>>>
>>>>> centerRho = rho
>>>>>
>>>>> call DMDAGetInfo(da,PETSC_NULL_INTEGER,mx,my,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,ierr)
>>>>>
>>>>> Hx = 1.d0 / (mx-1)
>>>>>
>>>>> Hy = 1.d0 / (my-1)
>>>>>
>>>>> HxdHy = Hx/Hy
>>>>>
>>>>> HydHx = Hy/Hx
>>>>>
>>>>> call DMDAGetCorners(da,xs,ys,PETSC_NULL_INTEGER,xm,ym,PETSC_NULL_INTEGER,ierr)
>>>>>
>>>>> do j=ys,ys+ym-1
>>>>>
>>>>> do i=xs,xs+xm-1
>>>>>
>>>>> row(MatStencil_i) = i
>>>>>
>>>>> row(MatStencil_j) = j
>>>>>
>>>>> call ComputeRho(i,j,mx,my,centerRho,rho)
>>>>>
>>>>> if (i.eq.0 .or. j.eq.0 .or. i.eq.mx-1 .or. j.eq.my-1) then
>>>>>
>>>>> v(1) = 2.0*rho*(HxdHy + HydHx)
>>>>>
>>>>> call MatSetValuesStencil(jac,i1,row,i1,row,v,INSERT_VALUES,ierr)
>>>>>
>>>>> else
>>>>>
>>>>> v(1) = -rho*HxdHy
>>>>>
>>>>> col(MatStencil_i,1) = i
>>>>>
>>>>> col(MatStencil_j,2) = j-1
>>>>>
>>>>> Cut and paste error above.
>>>>>
>>>>> Matt
>>>>>
>>>>> v(2) = -rho*HydHx
>>>>>
>>>>> col(MatStencil_i,2) = i-1
>>>>>
>>>>> col(MatStencil_j,2) = j
>>>>>
>>>>> v(3) = 2.0*rho*(HxdHy + HydHx)
>>>>>
>>>>> col(MatStencil_i,3) = i
>>>>>
>>>>> col(MatStencil_j,3) = j
>>>>>
>>>>> v(4) = -rho*HydHx
>>>>>
>>>>> col(MatStencil_i,4) = i+1
>>>>>
>>>>> col(MatStencil_j,4) = j
>>>>>
>>>>> v(5) = -rho*HxdHy
>>>>>
>>>>> col(MatStencil_i,5) = i
>>>>>
>>>>> col(MatStencil_j,5) = j+1
>>>>>
>>>>> call MatSetValuesStencil(jac,i1,row,i5,col,v,INSERT_VALUES,ierr)
>>>>>
>>>>> end if
>>>>>
>>>>> end do
>>>>>
>>>>> end do
>>>>>
>>>>> call MatAssemblyBegin(jac,MAT_FINAL_ASSEMBLY,ierr)
>>>>>
>>>>> call MatAssemblyEnd(jac,MAT_FINAL_ASSEMBLY,ierr)
>>>>>
>>>>> !call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,PETSC_NULL_INTEGER,PETSC_NULL_INTEGER,nullspace,ierr)
>>>>>
>>>>> !call MatSetNullSpace(jac,nullspace,ierr)
>>>>>
>>>>> !call MatNullSpaceDestroy(nullspace,ierr)
>>>>>
>>>>> end subroutine ComputeMatrix
>>>>>
>>>>> subroutine ComputeRho(i,j,mx,my,centerRho,rho)
>>>>>
>>>>> PetscInt i,j,mx,my
>>>>>
>>>>> PetscScalar rho,centerRho
>>>>>
>>>>> if ((i > mx/3.0) .and. (i < 2.0*mx/3.0) .and. (j > my/3.0) .and. (j < 2.0*my/3.0)) then
>>>>>
>>>>> rho = centerRho
>>>>>
>>>>> else
>>>>>
>>>>> rho = 1.0
>>>>>
>>>>> end if
>>>>>
>>>>>
>>>>> end subroutine ComputeRho
>>>>> --
>>>>> Yours sincerely,
>>>>>
>>>>> TAY wee-beng
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>>>> -- Norbert Wiener
>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>>> -- Norbert Wiener
>>>
>>>
>>>
>>> --
>>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>>> -- Norbert Wiener
>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
>> -- Norbert Wiener
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