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Discrete element models for the BODY package #962

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merged 29 commits into from Jul 20, 2018

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ndtrung81 commented Jun 22, 2018

Purpose

This PR contains the implementation of the discrete element models (DEM) for polygons and polyhedra following the models proposed by Langston and coworkers (Fraige et al., Particuology 2008, 6, 455-466, and Wang et al., Granular Matter 2011, 13, 1-12). In these DEM, the polygons and polyhedra are rounded at their vertices and edges by a specified diameter. The interaction between any pair of polygons and polyhedra is determined from a multiple contact model, as described in the mentioned references. The models (including the new atom styles, pair styles and related fixes) are part of the BODY package.

Author(s)

Trung Nguyen (Vietnam Academy of Science and Technology, now at Northwestern) - through discussion with, and suggestion by, Steve Plimpton.

Backward Compatibility

N/A

Implementation Notes

The current models do not take into account the contact history for friction forces as done in the mentioned references.

Post Submission Checklist

Please check the fields below as they are completed

  • The feature or features in this pull request is complete
  • Suitable new documentation files and/or updates to the existing docs are included
  • One or more example input decks are included
  • The source code follows the LAMMPS formatting guidelines

@ndtrung81 ndtrung81 self-assigned this Jun 22, 2018

@ndtrung81 ndtrung81 requested a review from sjplimp Jun 22, 2018

@sjplimp sjplimp assigned sjplimp and unassigned ndtrung81 Jul 9, 2018

Steven J. Plimpton
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sjplimp commented Jul 9, 2018

HI Trung - I made some small modifications to many of the files. In the doc files,
see my NOTE comments and Qs. Also, all the example files ran except
the pour3d example on 4 procs (it ran on 1 proc). It crashed on step 0.

@akohlmey akohlmey added this to the Stable Release Summer 2018 milestone Jul 16, 2018

Steven J. Plimpton and others added some commits Jul 16, 2018

Updated to the doc pages of body rounded/polygon and rounded/polyhedr…
…a and the pair style:

+ added examples for special cases with disks and rods for 2d, and spheres and rods for 3d,
+ corrected the definition of the cutoff distance in pair style command
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sjplimp commented Jul 18, 2018

@ndtrung81 I cleaned up your latest doc changes (removed my TRUNG comments)
and changed the name of the old pair_style body to body/nparticle (now that
there are several variants). I think this is ready to go, so am assigning to @akohlmey

@sjplimp sjplimp assigned akohlmey and unassigned sjplimp Jul 18, 2018

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akohlmey commented Jul 18, 2018

@sjplimp this needs some more work in the documentation. there are two issues:

  • redundant references to citations (sphinx website processing requires them to be unique across all files)
  • you did not update doc/src/lammps.book when renaming the existing body style (and the docs for it).

from the jenkins output at https://ci.lammps.org/job/lammps/job/pull-requests/job/build-docs-pr/1397/console

The HTML pages are in html.
############################################
Fraige
 - src/body.txt:450
 - src/pair_body_rounded_polygon.txt:132
Wang
 - src/body.txt:454
 - src/kspace_style.txt:353
 - src/pair_body_rounded_polyhedron.txt:126
Found 2 anchor label errors.
############################################

and

Converting write_data.txt ...
Converting write_dump.txt ...
Converting write_restart.txt ...
ERR005: Unable to find "pair_body.html"...
PAGES: 2260

                                                                               
BYTES: 16709078
Makefile:110: recipe for target 'pdf' failed
make: *** [pdf] Error 1
Steven J. Plimpton
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sjplimp commented Jul 18, 2018

doc changes done @akohlmey

@akohlmey akohlmey removed the request for review from sjplimp Jul 18, 2018

@akohlmey akohlmey assigned sjplimp and unassigned akohlmey Jul 18, 2018

@sjplimp sjplimp merged commit 5c21d2a into lammps:master Jul 20, 2018

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