[petsc-users] Create a DM given sets of IS's

[Justin Chang]

Okay so I managed to successfully do this by translating the IS's into a
PetscSection, assigning it to an empty DMShell, and then assigning that to
KSP.

However, I seem to be unable to rename the outer fields that aggregate two
or more inner fields. Consider this snippet of a four-field dual
porosity/permeability FEniCS/petsc4py code:

...

## Extract FEniCS dof layout, global indices ##
dof_total = np.array(W.dofmap().dofs())
dof_v1 = np.array(W.sub(0).dofmap().dofs())
dof_p1 = np.array(W.sub(1).dofmap().dofs())
dof_v2 = np.array(W.sub(2).dofmap().dofs())
dof_p2 = np.array(W.sub(3).dofmap().dofs())
offset = np.min(dof_total)

## Create PetscSection ##
section = PETSc.Section().create()
section.setNumFields(4)
section.setFieldName(0,'v1')
section.setFieldName(1,'p1')
section.setFieldName(2,'v2')
section.setFieldName(3,'p2')
section.setFieldComponents(0,1)
section.setFieldComponents(1,1)
section.setFieldComponents(2,1)
section.setFieldComponents(3,1)
section.setChart(0,len(dof_total))
for i in np.nditer(dof_v1):
  section.setDof(i-offset,1)
  section.setFieldDof(i-offset,0,1)
for i in np.nditer(dof_p1):
  section.setDof(i-offset,1)
  section.setFieldDof(i-offset,1,1)
for i in np.nditer(dof_v2):
  section.setDof(i-offset,1)
  section.setFieldDof(i-offset,2,1)
for i in np.nditer(dof_p2):
  section.setDof(i-offset,1)
  section.setFieldDof(i-offset,3,1)
section.setUp()

## Create DM and assign PetscSection ##
dm = PETSc.DMShell().create()
dm.setDefaultSection(section)
dm.setUp()

## Create KSP and assign DM ##
ksp = PETSc.KSP().create()
ksp.setDM(dm)
ksp.setDMActive(False)

### PETSc Command-line options ##
PETScOptions.set('ksp_monitor_true_residual')
PETScOptions.set('ksp_view')
PETScOptions.set('ksp_type','gmres')
PETScOptions.set('pc_type','fieldsplit')
PETScOptions.set('pc_fieldsplit_0_fields','0,1')
PETScOptions.set('pc_fieldsplit_1_fields','2,3')
PETScOptions.set('pc_fieldsplit_type','additive')
PETScOptions.set('fieldsplit_0_ksp_type','preonly')
PETScOptions.set('fieldsplit_0_pc_type','fieldsplit')
PETScOptions.set('fieldsplit_0_pc_fieldsplit_type','schur')
PETScOptions.set('fieldsplit_0_pc_fieldsplit_schur_fact_type','full')
PETScOptions.set('fieldsplit_0_pc_fieldsplit_schur_precondition','selfp')
PETScOptions.set('fieldsplit_0_fieldsplit_v1_ksp_type','preonly')
PETScOptions.set('fieldsplit_0_fieldsplit_v1_pc_type','bjacobi')
PETScOptions.set('fieldsplit_0_fieldsplit_p1_ksp_type','preonly')
PETScOptions.set('fieldsplit_0_fieldsplit_p1_pc_type','hypre')
PETScOptions.set('fieldsplit_1_ksp_type','preonly')
PETScOptions.set('fieldsplit_1_pc_type','fieldsplit')
PETScOptions.set('fieldsplit_1_pc_fieldsplit_type','schur')
PETScOptions.set('fieldsplit_1_pc_fieldsplit_schur_fact_type','full')
PETScOptions.set('fieldsplit_1_pc_fieldsplit_schur_precondition','selfp')
PETScOptions.set('fieldsplit_1_fieldsplit_v2_ksp_type','preonly')
PETScOptions.set('fieldsplit_1_fieldsplit_v2_pc_type','bjacobi')
PETScOptions.set('fieldsplit_1_fieldsplit_p2_ksp_type','preonly')
PETScOptions.set('fieldsplit_1_fieldsplit_p2_pc_type','hypre')

...

Is it possible to rename the outer splits (aka make
'-pc_fieldsplit_0_fields 0,1' be something like
'-pc_fieldsplit_micro_fields 0,1')?

Thanks,
Justin


On Mon, Dec 31, 2018 at 7:40 AM Matthew Knepley <knepley at gmail.com> wrote:

> On Mon, Dec 31, 2018 at 2:40 AM Justin Chang via petsc-users <
> petsc-users at mcs.anl.gov> wrote:
>
>> Hi all,
>>
>> I am solving a six field battery problem (concentration and potential for
>> each of the two solid and one electrolyte domains) and I want to experiment
>> with nested/recursice fieldsplitting. I have the IS's and am able to use
>> these to define my PCFieldSplitsSetIS(). However, I can imagine this
>> getting really messy from a programming standpoint, especially once I need
>> to add temperature into the mix, so it is my hope that I can translate
>> these index sets and fields into a DM (maybe DMShell?) so that I can just
>> rely on command line options to play around with various combinations of
>> field assignments and splits (e.g. -pc_fieldsplit_X_fields)
>>
>> However, it doesn't seem clear to me how I would create a DM when you
>> already know the IS's for each fields. If I understand functions like
>> DMCreateFieldDecomposition() correctly, it seems that it returns to you the
>> IS's and sub DM's associated with the original DM, whereas I want to do it
>> the other way around. Perhaps the "reversal" of something like
>> DMCreateFieldIS()
>> <https://www.mcs.anl.gov/petsc/petsc-dev/src/dm/interface/dm.c.html#DMCreateFieldIS>,
>> where you convert the IS into a PetscSection or is there an easier/better
>> way?
>>
>> Any thoughts/help appreciated!
>>
>
> Paul has recently done this for LibMesh. I believe that constructing a
> PetscSection is enough to get you minimally started. That allows
> DMCreateSubDM() to work by subsetting the Section, and that should allow
> the command line to work. CreateFieldDecomposition() should
> be removed I think.
>
>   Thanks,
>
>     Matt
>
>
>> Justin
>>
>
>
> --
> 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
>
> https://www.cse.buffalo.edu/~knepley/
> <http://www.cse.buffalo.edu/~knepley/>
>
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