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

Tue Jan 1 08:10:13 CST 2019

On Tue, Jan 1, 2019 at 5:06 AM Justin Chang <jychang48 at gmail.com> wrote:

> 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.
>

Right now you cannot do that because of the way that I check for the option:

https://bitbucket.org/petsc/petsc/src/0a5f382fff62a328ec919e3e9fe959e6cbbcf413/src/ksp/pc/impls/fieldsplit/fieldsplit.c#lines-369

I guess we could replace this by some search code that looked for any
option of that form and then read
out the splitname using scanf. Right now, I do not see a pattern search
function for the options database.

  Thanks,

    Matt

> 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/>
>>
>

-- 
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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