[petsc-users] Points in a ball

[Francesco Caimmi]

Dear all,

for an application I have in mind I have a domain divided in cells (more or less) and
for each cell centroid, say ci, I need to know which cell centroids are inside a
spherical neighbourhood of radius r centred at ci.

Were the centroids placed on regular grid, a typical value for the ratio of r over
the grid spacing would be something like 3 or 4.

However, since the discrete domain is actually not structured, I am using a DMPlex
object to manage the domain.

It is not very clear to me *if* and *how* I can tell the DMPlex to add ghost
points for all the points in such a spherical neighbourhood. If I were using DMDA
object I think I could just set the stencil width, but I wasn't able to figure out a
corresponding option/procedure for DMPlex (if it exists).

Any hint would be really really appreciated.

Best Regards,
--
Francesco Caimmi

Laboratorio di Ingegneria dei Polimeri
http://www.chem.polimi.it/polyenglab/

Politecnico di Milano - Dipartimento di Chimica,
Materiali e Ingegneria Chimica “Giulio Natta”

P.zza Leonardo da Vinci, 32
I-20133 Milano
Tel. [phone]
Fax [phone]

***@polimi.it
Skype: fmglcaimmi (please arrange meetings by e-mail)

[Matthew Knepley]

On Tue, Oct 20, 2015 at 2:53 AM, Francesco Caimmi <

Post by Francesco Caimmi
Dear all,
for an application I have in mind I have a domain divided in cells (more
or less) and for each cell centroid, say ci, I need to know which cell
centroids are inside a spherical neighbourhood of radius r centred at ci.
Were the centroids placed on regular grid, a typical value for the ratio
of r over the grid spacing would be something like 3 or 4.
However, since the discrete domain is actually not structured, I am using
a DMPlex object to manage the domain.
It is not very clear to me *if* and *how* I can tell the DMPlex to add
ghost points for all the points in such a spherical neighbourhood. If I
were using DMDA object I think I could just set the stencil width, but I
wasn't able to figure out a corresponding option/procedure for DMPlex (if
it exists).
Any hint would be really really appreciated.

The function that defines grid overlap is here:


https://bitbucket.org/petsc/petsc/src/fc309a34c451569cb3041ed38231443f9c022d73/src/dm/impls/plex/plexdistribute.c?at=master&fileviewer=file-view-default#plexdistribute.c-546

It calls a routine to define this overlap topologically


https://bitbucket.org/petsc/petsc/src/fc309a34c451569cb3041ed38231443f9c022d73/src/dm/impls/plex/plexdistribute.c?at=master&fileviewer=file-view-default#plexdistribute.c-612

You would have to modify this function to use a geometric criterion


https://bitbucket.org/petsc/petsc/src/fc309a34c451569cb3041ed38231443f9c022d73/src/dm/impls/plex/plexpartition.c?at=master&fileviewer=file-view-default#plexpartition.c-1470

If you do this, I can put it in as an option.

Thanks,

Matt

Post by Francesco Caimmi
Best Regards,
--
Francesco Caimmi
Laboratorio di Ingegneria dei Polimeri
http://www.chem.polimi.it/polyenglab/
Politecnico di Milano - Dipartimento di Chimica,
Materiali e Ingegneria Chimica “Giulio Natta”
P.zza Leonardo da Vinci, 32
I-20133 Milano
Tel. [phone]
Fax [phone]
Skype: fmglcaimmi (please arrange meetings by e-mail)