[gmx-users] Local Coordinates with DomDec

Justin Lemkul jalemkul at vt.edu
Fri Oct 13 01:17:27 CEST 2017

On 10/9/17 10:50 AM, Bradley Treece wrote:
> Hi All,
> I have a question about the handling of coordinates in local arrays with
> domain decomposition. It may take a moment to get to my actual question,
> but I want to make sure to be thorough with my explanation. Also, if I need
> to point this question toward a different mailing list, please let me know.
> By referencing the data structure reference page, I am aware that the
> mdatoms structure contains nr and homenr indicating the number of local and
> home atoms dealt with in the arrays x, f, and etc. I also know how to use
> the commrec to get back the global indices. This part may not be crucial to
> my question, but I also would like to check that I have this right. I
> searched high and low for the mdatoms->start integer but couldn't find it
> anywhere. I assume, and through careful checks, feel confident that this is
> part of an older version and it is the case that home atoms are contained
> in the first homenr atoms of an array; meaning the start parameter was
> somehow tied to the location of home atoms in the arrays but is now
> obsolete.
> My question is in regard to local atoms that are not part of the home set.
> Many of the position and force values for these behave as expected, but
> occasionally the three vectors for both are only zeros (almost as if they
> were uninitialized). I know for topological reasons that these atoms should
> not have coordinates of zero and presume that their forces should not be
> zero. I also have verified that they do fall below the nr cutoff of the
> index. I was wondering if anyone could point me to why this might be the
> case or correct any misunderstanding I have for how domdec manages these
> things.
> For reference, most of my testing takes place within the do_force function
> of src/gromacs/mdlib/sim_util.cpp  but I have done some checks elsewhere in
> the code to verify that it is not an issue isolated to this part of the
> code. I am also running 5.1.1 in case there are any version dependencies to
> take into account.

This is probably a question better asked on the gmx-developers mailing list.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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