[petsc-users] Convert a 3D DMDA sub-vector to a natural 2D vector

[Sajid Ali]

Hi PETSc-developers,

For an application, I'd like to extract a 2D slice from a 3D DMDA vector,
perform a `MatMult` on it (a discretized rotation on the 2D vector) and
place the resulting vector back into the 3D vector. The approach I'd taken
was to use `DMDACreatePatchIS` to create an IS that selects the slice (say
this slice is [:,:,n_z] with no loss of generality). This IS is then used
to extract the 2D slice via the `VecGetSubVector` utility. The issue that
arises from this scheme is that the extracted 2D vector does not represent
a flattened 2D vector, it is instead ordered as a DMDA vector (aka each
rank having the portion of vector it owns in a column major ordering). How
do I convert this DMDA ordered 2D subvector to a vector that represents a
flattened 2D array? Since I can't predict how the extracted sub-vector

While PETSc provides `DMDAGlobalToNatural` routines, those don't apply to
extracted sub-vectors and extracting the 2D slice from a natural vector
(filled by a scatter from the global vector) does not work either. On
the other hand, converting the output of DMDACreatePatchIS to a natural IS
via `AOPetscToApplicationIS` before extracting a subvector extracts the
wrong indices from the 3D vector.

Could someone tell me how I can achieve the desired goal (converting a 2D
vector ordered as per a 3D DMDA grid onto a natural flattened index) ?
Thanks in advance for the help!

PS : Should it help, I'm attaching a slightly modified version of
`src/dm/tests/ex53.c` to demonstrate the issue. The array I wish to obtain
(the [:,:,2]) slice is : `[196., 194., 192., 190., 198., 197., 196., 195.,
200., 200., 200.,200., 202., 203., 204., 205.]` (a row-major flattening of
the 2D slice or alternatively a column-major flattening). What I obtain
from the program (by creating the PatchIS and extracting the subvector)
instead is : `[0 (A)] 196,198,194,197 [1 (B)] 200,202,200,203 [2 (C)]
192,196,190,195 [3 (D)] 200,204,200,205` (where each square bracket
represents the rank and portion of the 2D vector being flattened via a
column-major formatting with the layout shown below)
|---------|
| A | C  |
| B | D  |
|---------|


Thank You,
Sajid Ali (he/him) | PhD Candidate
Applied Physics
Northwestern University
s-sajid-ali.github.io
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