[gmx-developers] Verlet-Tables integration
erik.lindahl at gmail.com
Wed Nov 14 15:04:16 CET 2018
... and for the low-level table code we (or somebody else :-) still need to
sit down and work through the math how we should specify tolerances (that
are used to set spacing) for arbitrary cases where the tabulated function
or its derivative has a zero-value in the relevant range.
On Wed, Nov 14, 2018 at 2:12 AM Berk Hess <hess at kth.se> wrote:
> I don't really think we need a usecase, but more people motivated to work
> on it.
> We have delayed the work also because we are waiting for a new non-bonded
> kernel structure. But we just as well start without that, since it will not
> take much work to port the additional tabulated kernels to a new framework.
> What is a dependency is a selecting the table index based on atom type
> (pairs). We want to get rid of the (mis)use of energy groups for this
> purpose in the group scheme.
> On 13/11/2018 23.53, Mark Abraham wrote:
> Not much has happened. I did some basic cleanup, and Erik has worked on
> some table classes in src/gromacs/tables. Alfredo has some old GPU kernels
> buried somewhere on Gerrit.
> It would be good to identify a use case that someone has interest in to
> e.g. contribute coding time, test cases, design idea sounding board. AFAIK
> none of the GROMACS core developers uses this feature, so their priorities
> tend to align elsewhere. However, we know it's useful to people, so we'd
> like to find a group that can work together to make it happen!
> Some of those dot points are a bit out of date, but the general list of
> things to do is about right.
> On Tue, Nov 13, 2018 at 3:48 PM Adriaan Riet <adriaan.riet at case.edu>
>> Hello everyone,
>> I know that Feature #1347 talks about the necessary steps to get tables
>> into Verlet (pasted below). I'm curious to know where this sits. I'm happy
>> to contribute where (if) I can, but don't see clearly where to jump in.
>> Have the points of the list been integrated into redmine feature requests?
>> Have any of these been implemented yet?
>> Adriaan Riet
>> Things to do (roughly in order):
>> - support regressiontests being able to read tables from grompp or
>> mdrun, so that new functionality in the code doesn't need matching changes
>> to the other repo for valid testing in the few cases where they use tables (
>> *CSTab* in group-scheme kernels)
>> - add integration tests, e.g. a Martini-style(?) non-bonded, and
>> several kinds of bonded interactions
>> - extract code from mdlib (particularly init_forcerec) so that it is
>> callable at grompp time, make sure grompp can issue all notes and warnings,
>> permit mdrun to repeat any of those that it might need to. Keep code for
>> making hardware-specific layout decisions in mdrun, because we won't know
>> whether the kernels need tables for CPUs or GPUs until then. If we can do
>> it without significant loss of accuracy, grompp should handle any
>> regularization of the user input (e.g. by constructing and testing CPU and
>> GPU tables, if necessary).
>> - move e.g. dihedral-interaction table reading to grompp, bump .tpr
>> version, write to .tpr, read in mdrun, add infrastructure to support gmx
>> check and gmx dump on new .tpr contents
>> - move angle- and bond-interaction table reading to grompp, probably
>> another .tpr version bump
>> - move short-range interaction tables to grompp for group scheme
>> - extend [pairs] to permit atom-type pairs to use an interaction
>> shape read from a table, e.g. from a file named on that line of the
>> topology. Should we have a per-pair-type scaling parameter? Requirements
>> for simulations that use only user tables, and those that mix user tables
>> with normal short-ranged interaction types probably differ.
>> - add Verlet-scheme table-support infrastructure
>> - add CPU kernels (hopefully in new scheme)
>> - add GPU kernels (recycle from Alfredo's patch in gerrit)
>> - after some time passes and master branch rebases enough, remove
>> workaround from regressiontests (which is anyway only needed for
>> group-scheme kernel testing)
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Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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