[petsc-users] Issue with Exporting and Reading Complex Vectors and Magnitude Vectors in PETSc and MATLAB

[Pierre Jolivet]

> On 1 Jul 2024, at 4:37 PM, maitri ksh <maitri.ksh at gmail.com> wrote:
> 
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> I need to export complex vectors data from PETSc and read them in MATLAB. However, I am encountering some issues with the data format and interpretation in MATLAB.  
> 
> code-snippet of the vector data export section:
> // Assemble the vectors before exporting
> ierr = VecAssemblyBegin(f); CHKERRQ(ierr);
> ierr = VecAssemblyEnd(f); CHKERRQ(ierr);
> 
> PetscViewer viewerf;
> // Save the complex vectors to binary files
> ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "output_f.dat", FILE_MODE_WRITE, &viewerf); CHKERRQ(ierr);
> ierr = VecView(f, viewerf); CHKERRQ(ierr);
> ierr = PetscViewerDestroy(&viewerf); CHKERRQ(ierr);
> 
> // Create vectors to store the magnitudes
> Vec f_magnitude;
> ierr = VecDuplicate(f, &f_magnitude); CHKERRQ(ierr);
> 
> // Get local portion of the vectors
> const PetscScalar *f_array;
> PetscScalar *f_magnitude_array;
> PetscInt n_local;
> 
> ierr = VecGetLocalSize(f, &n_local); CHKERRQ(ierr);
> ierr = VecGetArrayRead(f, &f_array); CHKERRQ(ierr);
> ierr = VecGetArray(f_magnitude, &f_magnitude_array); CHKERRQ(ierr);
> 
> // Compute the magnitude for each element
> for (int i = 0; i < n_local; i++) {
>     f_magnitude_array[i] = PetscAbsScalar(f_array[i]);
> }
> 
> // Restore arrays
> ierr = VecRestoreArrayRead(f, &f_array); CHKERRQ(ierr);
> ierr = VecRestoreArray(f_magnitude, &f_magnitude_array); CHKERRQ(ierr);
> 
> // Assemble the magnitude vectors
> ierr = VecAssemblyBegin(f_magnitude); CHKERRQ(ierr);
> ierr = VecAssemblyEnd(f_magnitude); CHKERRQ(ierr);
> 
> // Save the magnitude vectors to binary files
> PetscViewer viewerfmag;
> ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD, "output_f_mag.dat", FILE_MODE_WRITE, &viewerfmag); CHKERRQ(ierr);
> ierr = VecView(f_magnitude, viewerfmag); CHKERRQ(ierr);
> ierr = PetscViewerDestroy(&viewerfmag); CHKERRQ(ierr);
> 
> In MATLAB, I am using petscBinaryRead to read the data. The complex vectors are read, but only the real part is available. The magnitude vectors are however read as alternating zero and non-zero elements. What went wrong?
> How can I export the data correctly to MATLAB-accessible format? (I have not configured PETSc with Matlab as I was encountering library conflict issues)


How are you reading complex-valued binary files in MATLAB?
It is not the same as real-valued files, in particular, you must add the parameters 'complex', true to the PetscBinaryRead() call, type help PetscBinaryRead in the MATLAB console.

Thanks,
Pierre

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