[petsc-users] complex values in a bvp

[Smith, Barry F.]

   You have headed down the wrong track.

    You must ./configure PETSc with the option --with-scalar-type=complex to work with complex numbers and should declare the variables with PetscScalar just like in the example.

   Barry


> On Dec 4, 2017, at 3:26 PM, Swenson, Jennifer <jswenson at mail.smu.edu> wrote:
> 
> Dear PETSc Users, 
> 
> I have modified ex14 "Bratu nonlinear PDE in 3D" from the PETSc online examples (http://www.mcs.anl.gov/petsc/petsc-3.7/src/snes/examples/tutorials/ex14.c.html) to fit my current research problem. 
> 
> Notable changes of ex14 include reducing the size of the problem to 1D and using -snes_fd_color in the Makefile instead of the given "FormJacobian" function. When using this edited version of ex14, we obtained the desired outcome of a simple Stokes test problem. Now, we extend this work to our actual problem, a boundary value problem. Although the code compiles and runs, the output does not match our analytical results. 
> 
> We think that the issue is at least in part due to our equations including complex numbers via PETSC_i. We have noticed that there is a difference in output when using PetscScalar vs PetscComplex when testing PETSC_i:
> 
>   PetscScalar   test=10.0+PETSC_i*2.0; 
>   printf("%f+%fi\n", crealf(test), cimagf(test)); 
> The result is 10.000000+0.000000i.
> 
>   PetscComplex   test=10.0+PETSC_i*2.0; 
>   printf("%f+%fi\n", crealf(test), cimagf(test)); 
> The result is 10.000000+2.000000i.
> 
> This compelled us to change our variables (and even real parameters used with those variables) from PetscScalar to PetscComplex in FormFunction, while leaving our hz, dhz as PetscScalars:
>   
>   PetscScalar        hz, dhz;
>   PetscComplex   Q=0.5, h21=1.0;
>   PetscComplex   u, uz, w, wz, p, pz;
>  
>   hz     = 1.0/(PetscScalar)(Mx-1);
>   dhz    = 1.0/hz;
> 
> ...
> 
>   // u component of velocity
>   u   = x[i].x_vel;
>   uz  = (x[i].x_vel - x[i-1].x_vel)*dhz;
> 
>   // w component of velocity
>   w   = x[i].z_vel; 
>   wz  = (x[i].z_vel - x[i-1].z_vel)*dhz;
>       
>   // pressure
>   p  = x[i].pressure;
>   pz = (x[i].pressure - x[i-1].pressure)*dhz;
> 
>   f[i].x_vel    = (uz + PETSC_i*Q*w + 2.0*PETSC_i*Q*h21)/(dhz); 
>   f[i].z_vel    = (-p + 2.0*wz)/(dhz);
>   f[i].pressure = (PETSC_i*Q*u + wz)/(dhz); 
> 
> This switch from PetscScalar to PetscComplex did fix the discrepancy. Therefore, we also tried to change our Field variables from PetscScalar to PetscComplex:
> 
> typedef struct {
>   PetscScalar x_vel, z_vel, pressure; // variables for our system
> } Field;
> 
> However, an error is thrown when the program runs:
> 
> [0]PETSC ERROR: PetscMallocValidate: error detected at  SNESComputeFunction() line 2144 in /usr/local/src/petsc-dev/src/snes/interface/snes.c
> [0]PETSC ERROR: Memory at address 0x1af7d20 is corrupted
> [0]PETSC ERROR: Probably write past beginning or end of array
> [0]PETSC ERROR: Last intact block allocated in PetscLayoutSetUp() line 147 in /usr/local/src/petsc-dev/src/vec/is/utils/pmap.c
> [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
> [0]PETSC ERROR: Memory corruption: http://www.mcs.anl.gov/petsc/documentation/installation.html#valgrind
> [0]PETSC ERROR:  
> [0]PETSC ERROR: See http://www.mcs.anl.gov/petsc/documentation/faq.html for trouble shooting.
> [0]PETSC ERROR: Petsc Release Version 3.7.6, unknown 
> [0]PETSC ERROR: ./idea2.exe on a arch-linux2-c-debug named lovelace by jswenson Mon Dec  4 14:59:04 2017
> [0]PETSC ERROR: Configure options --prefix=/usr/local/petsc-dev --with-64-bit-indices=0 --with-fortran-interfaces=1 --CFLAGS=-O2 --CXXFLAGS=-O2 --FFLAGS=-O2 --download-hypre=yes --download-fftw=yes --download-superlu=yes --download-sundials=yes --download-metis=yes --download-parmetis=yes --download-superlu_dist=yes --download-spai=yes --download-sprng=1 --download-hdf5=yes --with-valgrind=0 --with-mpi-dir=/usr --with-shared-libraries=1 --with-c2html=0 --PETSC_ARCH=arch-linux2-c-debug
> [0]PETSC ERROR: #1 PetscMallocValidate() line 136 in /usr/local/src/petsc-dev/src/sys/memory/mtr.c
> [0]PETSC ERROR: #2 SNESComputeFunction() line 2144 in /usr/local/src/petsc-dev/src/snes/interface/snes.c
> [0]PETSC ERROR: #3 SNESSolve_NEWTONLS() line 181 in /usr/local/src/petsc-dev/src/snes/impls/ls/ls.c
> [0]PETSC ERROR: #4 SNESSolve() line 4005 in /usr/local/src/petsc-dev/src/snes/interface/snes.c
> 
> My specific questions are the following:
> 	• Is it important to have my Field variables PetscComplex or is PetscScalar sufficient?
> 	• Are there any foreseeable problems with using PETSC_i (or complex numbers in general) with this method from ex14? Do I need to somehow indicate to PETSc that I am using complex values? Am I just lacking an argument or an additional line?
> 	• Is there a nice way to save the solution (to be plotted) besides including -snes_monitor_solution ascii:myproblem.txt in the Makefile and writing an additional code to read and plot the results? For example, on a separate project, I really appreciated the functionality of -ts_monitor_solution_vtk  aks=.5%05D.vts in the Makefile. A similar technique would be useful here, if it exists. I have tried -snes_monitor_solution draw -draw_pause -1, but do not know if that works with complex values. Additionally, as far as I can tell, these plots cannot be saved.
> 
> Any other comments or insight would be greatly appreciated. Thank you for your time.
> 
> Sincerely,
> Jennifer Swenson