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From: Peter Zajac <peterzajac1@gm...>  20130509 17:43:57

Dear All, Is treatment in spherical coordinates an option in Libmesh? If not is there a plan to implement it in the near future? Thank you in advance PZ 
From: David Knezevic <dknezevic@se...>  20130509 17:48:45

I'm not sure I understand what you're getting at, but if you write the PDE in terms of (r,theta,phi), then you can just use libmesh in the standard way. You'll presumably get sin's, cos's and 1/r terms in the weak form, but that's no problem... On 05/09/2013 01:43 PM, Peter Zajac wrote: > Dear All, > > Is treatment in spherical coordinates an option in Libmesh? > If not is there a plan to implement it in the near future? > > Thank you in advance > > > PZ >  > Learn Graph Databases  Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: Paul T. Bauman <ptbauman@gm...>  20130509 17:57:35

What David said is correct (and how I currently deal with cylindrical coordinates). Nevertheless, while there are no formal plans, I've thought it would be nice to try and deal with alternative (to Cartesian) coordinate systems at the libMesh level. E.g. JxW comes premultiplied by r, curl/Laplacian/div/etc formulae have the right terms so that the same code could be used regardless of coordinate system, etc. Alas, it hasn't been high enough priority for me to spend any time thinking about it and proposing how to do it, e.g. whether it should be an FE type, etc. That said, Peter, if you wanted to take a crack at it, I (and probably others) would be happy to give guidance. On Thu, May 9, 2013 at 12:48 PM, David Knezevic <dknezevic@...>wrote: > I'm not sure I understand what you're getting at, but if you write the > PDE in terms of (r,theta,phi), then you can just use libmesh in the > standard way. You'll presumably get sin's, cos's and 1/r terms in the > weak form, but that's no problem... > > > > On 05/09/2013 01:43 PM, Peter Zajac wrote: > > Dear All, > > > > Is treatment in spherical coordinates an option in Libmesh? > > If not is there a plan to implement it in the near future? > > > > Thank you in advance > > > > > > PZ > > >  > > Learn Graph Databases  Download FREE O'Reilly Book > > "Graph Databases" is the definitive new guide to graph databases and > > their applications. This 200page book is written by three acclaimed > > leaders in the field. The early access version is available now. > > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > > _______________________________________________ > > Libmeshusers mailing list > > Libmeshusers@... > > https://lists.sourceforge.net/lists/listinfo/libmeshusers > > > >  > Learn Graph Databases  Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers > 
From: Roy Stogner <roystgnr@ic...>  20130509 18:02:00

On Thu, 9 May 2013, Paul T. Bauman wrote: > What David said is correct (and how I currently deal with cylindrical > coordinates). Nevertheless, while there are no formal plans, I've thought > it would be nice to try and deal with alternative (to Cartesian) coordinate > systems at the libMesh level. E.g. JxW comes premultiplied by r, > curl/Laplacian/div/etc formulae have the right terms so that the same code > could be used regardless of coordinate system, etc. Alas, it hasn't been > high enough priority for me to spend any time thinking about it and > proposing how to do it, e.g. whether it should be an FE type, etc. I looked into this too; it's been a long while, IIRC I ran into issues with covariant vs. contravariant vectors in some formulation that made it nonobvious how to enable coordinatesystemindependent code. > That said, Peter, if you wanted to take a crack at it, I (and probably > others) would be happy to give guidance. Likewise.  Roy 
From: PETER ZAJAC <peterzajac1@gm...>  20130509 18:22:23

David, I was worried about the volume element for integration. If I use explicit transformations of coordinates to spherical how would I make sure that the volume element for integration changes accordingly. Paul, I am not sure i ll be the best person for the job. With all my honesty (and considering my level of expertise in Libmesh) I might do more harm than good ;) Thank you Peter On May 9, 2013, at 10:57, "Paul T. Bauman" <ptbauman@...> wrote: > What David said is correct (and how I currently deal with cylindrical > coordinates). Nevertheless, while there are no formal plans, I've thought > it would be nice to try and deal with alternative (to Cartesian) coordinate > systems at the libMesh level. E.g. JxW comes premultiplied by r, > curl/Laplacian/div/etc formulae have the right terms so that the same code > could be used regardless of coordinate system, etc. Alas, it hasn't been > high enough priority for me to spend any time thinking about it and > proposing how to do it, e.g. whether it should be an FE type, etc. > > That said, Peter, if you wanted to take a crack at it, I (and probably > others) would be happy to give guidance. > > > On Thu, May 9, 2013 at 12:48 PM, David Knezevic > <dknezevic@...>wrote: > >> I'm not sure I understand what you're getting at, but if you write the >> PDE in terms of (r,theta,phi), then you can just use libmesh in the >> standard way. You'll presumably get sin's, cos's and 1/r terms in the >> weak form, but that's no problem... >> >> >> >> On 05/09/2013 01:43 PM, Peter Zajac wrote: >>> Dear All, >>> >>> Is treatment in spherical coordinates an option in Libmesh? >>> If not is there a plan to implement it in the near future? >>> >>> Thank you in advance >>> >>> >>> PZ >>> >>  >>> Learn Graph Databases  Download FREE O'Reilly Book >>> "Graph Databases" is the definitive new guide to graph databases and >>> their applications. This 200page book is written by three acclaimed >>> leaders in the field. The early access version is available now. >>> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may >>> _______________________________________________ >>> Libmeshusers mailing list >>> Libmeshusers@... >>> https://lists.sourceforge.net/lists/listinfo/libmeshusers >> >> >> >>  >> Learn Graph Databases  Download FREE O'Reilly Book >> "Graph Databases" is the definitive new guide to graph databases and >> their applications. This 200page book is written by three acclaimed >> leaders in the field. The early access version is available now. >> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may >> _______________________________________________ >> Libmeshusers mailing list >> Libmeshusers@... >> https://lists.sourceforge.net/lists/listinfo/libmeshusers >> >  > Learn Graph Databases  Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > _______________________________________________ > Libmeshusers mailing list > Libmeshusers@... > https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: David Knezevic <dknezevic@se...>  20130509 18:29:19

On 05/09/2013 02:22 PM, PETER ZAJAC wrote: > David, > > I was worried about the volume element for integration. If I use explicit transformations of coordinates to spherical how would I make sure that the volume element for integration changes accordingly. Cartesian > spherical is just a change of coordinates, so if you take that into account properly in the weak form then everything is fine. In particular, you need to account for:  the change of measure, which gives an extra r^2 * \sin(\phi) factor, if memory serves  the change of variables in the gradient terms It would be nice to automate this so that it is automatically included in libMesh's JxW and dphi, which is what Paul was referring to. But the easiest thing for you in the short term would be to just explicitly deal with the change of variables yourself. David On May 9, 2013, at 10:57, "Paul T. Bauman" <ptbauman@...> wrote: >> What David said is correct (and how I currently deal with cylindrical >> coordinates). Nevertheless, while there are no formal plans, I've thought >> it would be nice to try and deal with alternative (to Cartesian) coordinate >> systems at the libMesh level. E.g. JxW comes premultiplied by r, >> curl/Laplacian/div/etc formulae have the right terms so that the same code >> could be used regardless of coordinate system, etc. Alas, it hasn't been >> high enough priority for me to spend any time thinking about it and >> proposing how to do it, e.g. whether it should be an FE type, etc. >> >> That said, Peter, if you wanted to take a crack at it, I (and probably >> others) would be happy to give guidance. >> >> >> On Thu, May 9, 2013 at 12:48 PM, David Knezevic >> <dknezevic@...>wrote: >> >>> I'm not sure I understand what you're getting at, but if you write the >>> PDE in terms of (r,theta,phi), then you can just use libmesh in the >>> standard way. You'll presumably get sin's, cos's and 1/r terms in the >>> weak form, but that's no problem... >>> >>> >>> >>> On 05/09/2013 01:43 PM, Peter Zajac wrote: >>>> Dear All, >>>> >>>> Is treatment in spherical coordinates an option in Libmesh? >>>> If not is there a plan to implement it in the near future? >>>> >>>> Thank you in advance >>>> >>>> >>>> PZ >>>> >>>  >>>> Learn Graph Databases  Download FREE O'Reilly Book >>>> "Graph Databases" is the definitive new guide to graph databases and >>>> their applications. This 200page book is written by three acclaimed >>>> leaders in the field. The early access version is available now. >>>> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may >>>> _______________________________________________ >>>> Libmeshusers mailing list >>>> Libmeshusers@... >>>> https://lists.sourceforge.net/lists/listinfo/libmeshusers >>> >>> >>>  >>> Learn Graph Databases  Download FREE O'Reilly Book >>> "Graph Databases" is the definitive new guide to graph databases and >>> their applications. This 200page book is written by three acclaimed >>> leaders in the field. The early access version is available now. >>> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may >>> _______________________________________________ >>> Libmeshusers mailing list >>> Libmeshusers@... >>> https://lists.sourceforge.net/lists/listinfo/libmeshusers >>> >>  >> Learn Graph Databases  Download FREE O'Reilly Book >> "Graph Databases" is the definitive new guide to graph databases and >> their applications. This 200page book is written by three acclaimed >> leaders in the field. The early access version is available now. >> Download your free book today! http://p.sf.net/sfu/neotech_d2d_may >> _______________________________________________ >> Libmeshusers mailing list >> Libmeshusers@... >> https://lists.sourceforge.net/lists/listinfo/libmeshusers 
From: Peter Zajac <peterzajac1@gm...>  20130509 20:21:27

On Thu, May 9, 2013 at 11:29 AM, David Knezevic <dknezevic@...>wrote: > On 05/09/2013 02:22 PM, PETER ZAJAC wrote: > >> David, >> >> I was worried about the volume element for integration. If I use >> explicit transformations of coordinates to spherical how would I make sure >> that the volume element for integration changes accordingly. >> > > Cartesian > spherical is just a change of coordinates, so if you take > that into account properly in the weak form then everything is fine. In > particular, you need to account for: >  the change of measure, which gives an extra r^2 * \sin(\phi) factor, if > memory serves >  the change of variables in the gradient terms > > It would be nice to automate this so that it is automatically included in > libMesh's JxW and dphi, which is what Paul was referring to. But the > easiest thing for you in the short term would be to just explicitly deal > with the change of variables yourself. > > Great. Thank you. This will work. PZ > David > > > > > > > On May 9, 2013, at 10:57, "Paul T. Bauman" <ptbauman@...> wrote: > >> What David said is correct (and how I currently deal with cylindrical >>> coordinates). Nevertheless, while there are no formal plans, I've thought >>> it would be nice to try and deal with alternative (to Cartesian) >>> coordinate >>> systems at the libMesh level. E.g. JxW comes premultiplied by r, >>> curl/Laplacian/div/etc formulae have the right terms so that the same >>> code >>> could be used regardless of coordinate system, etc. Alas, it hasn't been >>> high enough priority for me to spend any time thinking about it and >>> proposing how to do it, e.g. whether it should be an FE type, etc. >>> >>> That said, Peter, if you wanted to take a crack at it, I (and probably >>> others) would be happy to give guidance. >>> >>> >>> On Thu, May 9, 2013 at 12:48 PM, David Knezevic >>> <dknezevic@...>**wrote: >>> >>> I'm not sure I understand what you're getting at, but if you write the >>>> PDE in terms of (r,theta,phi), then you can just use libmesh in the >>>> standard way. You'll presumably get sin's, cos's and 1/r terms in the >>>> weak form, but that's no problem... >>>> >>>> >>>> >>>> On 05/09/2013 01:43 PM, Peter Zajac wrote: >>>> >>>>> Dear All, >>>>> >>>>> Is treatment in spherical coordinates an option in Libmesh? >>>>> If not is there a plan to implement it in the near future? >>>>> >>>>> Thank you in advance >>>>> >>>>> >>>>> PZ >>>>> >>>>> **** >>>>  >>>> >>>>> Learn Graph Databases  Download FREE O'Reilly Book >>>>> "Graph Databases" is the definitive new guide to graph databases and >>>>> their applications. This 200page book is written by three acclaimed >>>>> leaders in the field. The early access version is available now. >>>>> Download your free book today! http://p.sf.net/sfu/neotech_**d2d_may<http://p.sf.net/sfu/neotech_d2d_may>; >>>>> ______________________________**_________________ >>>>> Libmeshusers mailing list >>>>> Libmeshusers@...**sourceforge.net<Libmeshusers@...> >>>>> https://lists.sourceforge.net/**lists/listinfo/libmeshusers<https://lists.sourceforge.net/lists/listinfo/libmeshusers>; >>>>> >>>> >>>> >>>> **** >>>>  >>>> Learn Graph Databases  Download FREE O'Reilly Book >>>> "Graph Databases" is the definitive new guide to graph databases and >>>> their applications. This 200page book is written by three acclaimed >>>> leaders in the field. The early access version is available now. >>>> Download your free book today! http://p.sf.net/sfu/neotech_**d2d_may<http://p.sf.net/sfu/neotech_d2d_may>; >>>> ______________________________**_________________ >>>> Libmeshusers mailing list >>>> Libmeshusers@...**sourceforge.net<Libmeshusers@...> >>>> https://lists.sourceforge.net/**lists/listinfo/libmeshusers<https://lists.sourceforge.net/lists/listinfo/libmeshusers>; >>>> >>>> **** >>>  >>> Learn Graph Databases  Download FREE O'Reilly Book >>> "Graph Databases" is the definitive new guide to graph databases and >>> their applications. This 200page book is written by three acclaimed >>> leaders in the field. The early access version is available now. >>> Download your free book today! http://p.sf.net/sfu/neotech_**d2d_may<http://p.sf.net/sfu/neotech_d2d_may>; >>> ______________________________**_________________ >>> Libmeshusers mailing list >>> Libmeshusers@...**sourceforge.net<Libmeshusers@...> >>> https://lists.sourceforge.net/**lists/listinfo/libmeshusers<https://lists.sourceforge.net/lists/listinfo/libmeshusers>; >>> >> > 
From: David Knezevic <dknezevic@se...>  20130509 20:26:51

On 05/09/2013 04:21 PM, Peter Zajac wrote: > > On Thu, May 9, 2013 at 11:29 AM, David Knezevic > <dknezevic@... <mailto:dknezevic@...>> wrote: > > On 05/09/2013 02:22 PM, PETER ZAJAC wrote: > > David, > > I was worried about the volume element for integration. If I > use explicit transformations of coordinates to spherical how > would I make sure that the volume element for integration > changes accordingly. > > > Cartesian > spherical is just a change of coordinates, so if you > take that into account properly in the weak form then everything > is fine. In particular, you need to account for: >  the change of measure, which gives an extra r^2 * \sin(\phi) > factor, if memory serves >  the change of variables in the gradient terms > > It would be nice to automate this so that it is automatically > included in libMesh's JxW and dphi, which is what Paul was > referring to. But the easiest thing for you in the short term > would be to just explicitly deal with the change of variables > yourself. > > > Great. Thank you. This will work. P.S. You'll also need to impose periodic boundary conditions in the azimuthal direction. 
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