[petsc-dev] DMDA VTK viewer regression: field names missing

[Matthew Knepley]

On Thu, Mar 28, 2019 at 12:47 PM Dave May via petsc-dev <
petsc-dev at mcs.anl.gov> wrote:

> I'd advocate flattening everything as a scalar field. Why?
> 1) the xml vtk formats for vector only work if ncomponents = 3, so for a
> 2d field you have to insert a dummy set of zero values for the z component
> 2) its simple to build vector fields which paraview can render if the
> scalar fields are properly named (and inserting the k-components with
> zeroes if required)
> 3) It will work for case 2 and case 3
>

The painful thing on the other side is that you cannot plot glyphs for the
vector field without
defining it by hand with the calculator. This was enough to kick me in the
ass and define it.

  Matt


> On Thu, 28 Mar 2019 at 17:13, Patrick Sanan <patrick.sanan at gmail.com>
> wrote:
>
>>
>>
>> Am Do., 28. März 2019 um 09:10 Uhr schrieb Patrick Sanan <
>> patrick.sanan at gmail.com>:
>>
>>> Agreed that
>>> - these viewers should prioritize being quick and viewable with as
>>> little post-processing as possible
>>> - this change is bad in throwing away the field name metadata
>>>
>>> The trick here seems to be knowing what the user is representing with a
>>> multi-dof DMDA, and being faithful to that in the output file. This could be
>>> 1. a single scalar field
>>> 2. multiple scalar fields (which the user wants to store interlaced, as
>>> opposed to using a DMComposite)
>>> 3. a single vector-valued field
>>> 4. multiple scalar or vector fields, of arbitrary dimensions (adding up
>>> the total dof of the DMDA), interlaced
>>>
>>> Case 4 can be approximated by case 2, as in Jed's initial example.
>>> I believe that the PetscSection / PetscField framework was introduced to
>>> more generally support this, at least for DMPlex.
>>>
>> PetscField isn't a thing - I meant the various PetscSection*Field*()
>> functions.
>>
>>>
>>> My PR broke (or at least harmed) case 2, to allow for more-convenient
>>> handling of case 3.
>>> As Jed says, this was motivated by requiring less post-processing to
>>> view a vector field in Paraview,
>>> but it created the need for more post-processing for the
>>> multiple-scalar-field approach.
>>>
>>> Options to fix this include
>>> a. Revert to the old behavior
>>> b. Provide options to the user to distinguish between cases 2 and 3
>>> (multiple scalar fields vs vector field)
>>> c. Try to automatically detect which type of output (say, check if any
>>> field names have been set)
>>> d. Investigate supporting case 4 (arbitrary fields of arbitrary
>>> dimension) by using PetscSection
>>> e. (If even possible) Properly name the components of a vector in a VTK
>>> file
>>>
>>> Before I start poking around, I'm shaky on assessing options d and e!
>>>
>>>
>>>
>>>
>>> Am Do., 28. März 2019 um 08:21 Uhr schrieb Dave May via petsc-dev <
>>> petsc-dev at mcs.anl.gov>:
>>>
>>>>
>>>>
>>>> On Thu, 28 Mar 2019 at 15:42, Jed Brown via petsc-dev <
>>>> petsc-dev at mcs.anl.gov> wrote:
>>>>
>>>>> Matthew Knepley <knepley at gmail.com> writes:
>>>>>
>>>>> > On Wed, Mar 27, 2019 at 10:56 PM Jed Brown via petsc-dev <
>>>>> > petsc-dev at mcs.anl.gov> wrote:
>>>>> >
>>>>> >> Prior to this PR, which was merged for 3.10
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> https://bitbucket.org/petsc/petsc/pull-requests/1029/dmda-vtk-viewing-output-multiple-dof/diff
>>>>> >>   https://bitbucket.org/petsc/petsc/commits/ea2d7708fa6
>>>>> >>
>>>>> >> we could have files that look like the following, and thus were
>>>>> easy to
>>>>> >> navigate in Paraview and Visit.
>>>>> >>
>>>>> >
>>>>> > Tell me if I am wrong (since I do not run it this way). I think the
>>>>> point
>>>>> > of Patrick's change is a good one, and
>>>>> > necessary to view things with DMStag.
>>>>>
>>>>> Or maybe just necessary to avoid needing to use multiple files or add
>>>>> filters.
>>>>>
>>>>> > What Jed dislikes, rightly, is that some metadata has gone missing.
>>>>> > Does Xdmf allow you to name the components? The way I do this
>>>>> > petsc_gen_xdmf.py is to write the whole thing as Patrick does, but
>>>>> > then create views into the data using the component names. It sound
>>>>> > like this should be doable here.
>>>>>
>>>>> Perhaps.  A key reason for using VTK viewers is that they're relatively
>>>>> quick and foolproof compared to formats that need libraries and/or
>>>>> auxiliary files.
>>>>
>>>>
>>>> I completely agree with the above comment. I consider these files as
>>>> "instant and usable viz".
>>>>
>>>> I'd like both the dm field names and the vec name to be used to define
>>>> the vtk field names.
>>>>
>>>> One idea:
>>>>   vecname_fieldname
>>>> falling back to
>>>>   "field"%d_fieldname, where %d is the index of the vector to be
>>>> written (we can determine this as all vectors are cached to support
>>>> appended data)
>>>> faillng back to
>>>>   "field"%d_%d
>>>> where the last index here is the block index.
>>>>
>>>> These names should work with unnamed dm fields, multiple vectors
>>>> obtained from DMCreateGlobalVector or VecDuplicate. It does not account
>>>> immediately address what happens if two vectors produce identical fieldname
>>>> - code should be added for that using the last fall back. I think this
>>>> would be better than using the stringifed memory address which was used
>>>> before Patrick's PR. That suffered from the same issue Jed raised at the
>>>> start of this thread (users must remember the order vecs were written)
>>>>
>>>> Thanks
>>>> Dave
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>

-- 
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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