Hello --

After you generate the mesh with Gamer, you will need to manually edit the boundary conditions to provide connectivity between the edges of the mesh.  If you have a simple mesh file that you can send to me, I can send you the edited file that shows the connections.


Nathan Baker
Laboratory Fellow and Technical Group Manager
Applied Statistics and Computational Modeling Group
Pacific Northwest National Laboratory

From: Yuqing Deng <yuqing.deng@gmail.com>
Date: Monday, May 5, 2014 at 11:34
To: APBS-USERS mailing list <apbs-users@googlegroups.com>
Cc: APBS-USERS mailing list <apbs-users@lists.sourceforge.net>, Nathan Baker <nathan.baker@pnnl.gov>
Subject: Re: [apbs-users] No periodic boundary condition for APBS?

Hi Nathan,

I built APBS 1.4 with FEM support.  Would you post the instructions on how to use PBC with FEM?
I tried to generate a mesh with MolecularMesh tool from Gamer but it APBS complains that atom 0 is not inside the mesh.

Thank you,


On Thursday, December 5, 2013 9:41:24 AM UTC-5, Baker, Nathan wrote:

Hi Nuo –


Periodic boundary conditions are available in the finite element features of APBS – but require some guidance to use.  We haven’t implemented periodic boundary conditions in the finite difference multigrid part of the code because it would require some substantial changes.  However, we are considering non-multigrid (and therefore less scalable) approaches for periodic boundary conditions.  Would this be of interest to you?  It would be great to collaborate on this.





Nathan Baker

Laboratory Fellow

Pacific Northwest National Laboratory




From: Nuo Wang [mailto:woli...@gmail.com]
Sent: Wednesday, December 04, 2013 4:54 PM
To: apbs-...@googlegroups.com
Subject: [apbs-users] No periodic boundary condition for APBS?


Hi APBS developers,


From googling, I know that there is no periodic boundary condition in APBS yet (right?). But this seems to be a useful feature for a number of problems, so I have 2 questions here:


1. Will the next release contain periodic boundary condition?

2. May I know why the periodic boundary condition hasn't been implemented? a lack of public interest? or hard to program?


I ask this because I'm thinking of adding a periodic boundary condition feature myself.


Thanks a lot!