Diffusion lammps (master) History

History
master20ae05055dbb04054f0c1c6…

Mar 28 2017

fix memory leak via NeighListKokkos::clean_copy()
20ae05055dbb
·Dan Ibanez on Mar 28 2017, 19:38.

Mar 27 2017

Make read_restart evenly divide the work of reading when using mpiio. Currently…
661bd37e15bc
·Tim Mattox on Mar 27 2017, 22:03.
USER-DPD Kokkos: tighten up the SSA data allocation to what is needed. A future…
0463923e330b
·Tim Mattox on Mar 27 2017, 18:04.
Now with the correct math, make read_restart properly size the atom_vec_* data
28784a4ce2de
·Tim Mattox on Mar 27 2017, 15:38.
Make read_restart properly size the atom_vec_* data when reading via mpiio
5f0823172c4a
·Tim Mattox on Mar 27 2017, 12:56.
USER-DPD: bugfix for an array that changed length in the non-kokkos version.
b418b46a03ac
·Tim Mattox on Mar 27 2017, 12:56.

Mar 21 2017

make RK solver check in fix_rx_kokkos.cpp be as lenient as in fix_rx.cpp NOTE…
3c91f9734dbb
·Tim Mattox on Mar 21 2017, 22:12.

Mar 20 2017

Merge branch 'USER-DPD_GBhacks' into USER-DPD_GBhacks_cps
4ad1c82fcf1e
·Tim Mattox on Mar 20 2017, 19:37.
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
ce94d7a4dfac
·Stan Moore on Mar 20 2017, 19:16.
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
2c93065786a1
·Stan Moore on Mar 20 2017, 19:13.
Merge pull request #426 from dstelter92/master
d496c0fdfa9f
·sjplimp / GitHub on Mar 20 2017, 15:57.
re-ran example with fixed exchanges
5c39dfd74089
·dstelter92 on Mar 20 2017, 14:22.
Teff and exchange bugfix, as per Greg Dignon to match python examples
5b842f0010a7
·dstelter92 on Mar 20 2017, 14:15.
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bring in bugfix
20de98e898f0
·Tim Mattox on Mar 20 2017, 02:22.
USER-DPD Kokkos: bugfix, add a misisng line of code in pair_exp6_rx_kokkos.cpp
a68f3a93e53a
·Tim Mattox on Mar 20 2017, 02:12.

Mar 18 2017

Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bugfix for bonds
b3c46b7269db
·Tim Mattox on Mar 18 2017, 01:15.
USER-DPD Kokkos: bugfix for npair_ssa_kokkos.cpp corresponding to 0cd3f0cd
fff43a4604a2
·Tim Mattox on Mar 18 2017, 00:33.
USER-DPD: bugfix for npair_half_bin_newton_ssa when bonds are involved. Only…
0cd3f0cd63f2
·Tim Mattox on Mar 18 2017, 00:22.

Mar 17 2017

Added ONE-TYPE template capability to vectorized_operator and cleaned up timers.
75670244bb5d
·Christopher P. Stone on Mar 17 2017, 22:02.
Kokkos/pair_exp6_rx_kokkos optimized for SIMD on the inner j-loop.
64fdb1f528bc
·Christopher P. Stone on Mar 17 2017, 20:52.
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, as of patch 17March17
eb1a4d11ddf4
·Tim Mattox on Mar 17 2017, 20:18.
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
1c749d5cf590
·Stan Moore on Mar 17 2017, 19:09.
patch 17Mar17
4a90bca7a3b4
·Steve Plimpton on Mar 17 2017, 18:29.
Merge pull request #424 from timattox/dpd_restart_fix
9f35b764f8cc
·sjplimp / GitHub on Mar 17 2017, 18:19.
Merge pull request #423 from timattox/master_bugfix_irregular
7ca5dce2f56c
·sjplimp / GitHub on Mar 17 2017, 18:18.
Merge pull request #421 from akohlmey/memory-output
fcc3b3bd365d
·sjplimp / GitHub on Mar 17 2017, 18:18.
Merge pull request #420 from rbberger/doc_anchor_check
53a3877c3d3e
·sjplimp / GitHub on Mar 17 2017, 18:17.
Merge pull request #419 from rbberger/python_fixes
a936b7b2ab27
·sjplimp / GitHub on Mar 17 2017, 18:16.
Merge pull request #416 from lukin17/filter_corotate
a91b851f3d40
·sjplimp / GitHub on Mar 17 2017, 18:14.
Remove unneeded restart_peratom flags
d31c591b60f7
·Stan Moore on Mar 17 2017, 16:40.
add support for MPI_Request_free() to MPI STUBS library
ae5ebf600189
·Axel Kohlmeyer on Mar 17 2017, 16:40.
Revert "In irregular.cpp use simpler and slightly faster…
7fb741d53da8
·Axel Kohlmeyer on Mar 17 2017, 16:35.
Merge remote-tracking branch 'thunder/USER-DPD_kokkos_gb_test' into USER…
a719f41426e0
·Christopher P. Stone on Mar 17 2017, 15:26.
Merge remote-tracking branch 'thunder/USER-DPD_GBhacks' into USER…
ba069fb755a4
·Christopher P. Stone on Mar 17 2017, 15:11.
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks, bring in MPI deadlock fix
4a7bc115cbbd
·Tim Mattox on Mar 17 2017, 08:24.
Merge branch 'master_bugfix_irregular' into USER-DPD_kokkos
5ea096d08cdc
·Tim Mattox on Mar 17 2017, 08:19.
In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()
8e75616c144d
·Tim Mattox on Mar 17 2017, 08:02.
BUGFIX: Prevent possible deadlock in Irregular::create_atom and create_data
411c069ba66f
·Tim Mattox on Mar 17 2017, 08:02.
ignore package pair style
ac82d041cc44
·Axel Kohlmeyer on Mar 17 2017, 04:12.
Correct off-by-one error in line number reported
621d7d5ce0f2
·Richard Berger on Mar 17 2017, 04:05.
Remove some duplicate anchors in documentation
1bb9c7da42e5
·Richard Berger on Mar 17 2017, 03:36.
Cleaned up the non-kokkos part of KOKKOS/pair_exp6_rx_kokkos.cpp
ec192a95cb14
·Christopher P. Stone on Mar 17 2017, 03:28.
Add anchor_check to doc Makefile
f893104b18d1
·Richard Berger on Mar 17 2017, 03:21.
Add utility to detect duplicate anchors in documentation files
efb2a942e046
·Richard Berger on Mar 17 2017, 03:21.
Non-kokkos candidate of PairExp6rxKokkos::getMixingWeights to improve…
f5b7361ef6b6
·Christopher P. Stone on Mar 17 2017, 02:31.

Mar 16 2017

improve memory usage reporting in info and output class
070ce33a13df
·Axel Kohlmeyer on Mar 16 2017, 23:35.
add fix filter/corotate to some administrative files
f604f86cfcd4
·Axel Kohlmeyer on Mar 16 2017, 20:08.
simplify and shorten examples for fix filter/corotate and combine into a single…
bed288339e74
·Axel Kohlmeyer on Mar 16 2017, 20:02.
fix some more code formatting issues, add newline at EOF
1995f434f3d3
·Axel Kohlmeyer on Mar 16 2017, 19:24.
Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull…
db0281b4df0b
·Axel Kohlmeyer on Mar 16 2017, 17:14.
Fixing index issue in pair_exp6_rx_kokkos
acdb932c4ec5
·Stan Moore on Mar 16 2017, 16:28.
Merge remote-tracking branch 'upstream/master' into filter_corotate
2f5e711acd82
·lukin17 on Mar 16 2017, 10:00.
Fixed coding style.
bdb7669e2742
·lukin17 on Mar 16 2017, 09:44.
Added Python matplotlib plot example
cda821389250
·Richard Berger on Mar 16 2017, 06:41.
Improve Python 3 compatibility of pizza tools and simplify read_snapshot code
ef940d226c33
·Richard Berger on Mar 16 2017, 06:38.
Fix dump cfg in vizplotgui_atomeye.py example
36da9223ec43
·Richard Berger on Mar 16 2017, 03:55.
Fix space/tab error in pizza/gl.py
eb29ef32b1b9
·Richard Berger on Mar 16 2017, 03:43.
Fix dump cfg in viz_atomeye.py example
29550d472d23
·Richard Berger on Mar 16 2017, 03:31.
Document property 'uses_exceptions' of Python interface
79cae51156ad
·Richard Berger on Mar 16 2017, 03:20.
Fixes lammps_create_atoms library function and its Python interface variant
a210867025e1
·Richard Berger on Mar 16 2017, 03:13.
Fix Python 3 compatibility by encoding strings passed as c_char_p
0262a54ecfeb
·Richard Berger on Mar 16 2017, 03:00.
Merge branch 'USER-DPD_kokkos' into USER-DPD_GBhacks
ce9b3f4fcb7f
·Tim Mattox on Mar 16 2017, 00:17.

Mar 15 2017

Merge branch 'filter_corotate' of https://github.com/lukin17/lammps into pull…
0d8f74f0c52e
·Axel Kohlmeyer on Mar 15 2017, 23:54.
Adding gb_test
7ebed717de98
·Stan Moore on Mar 15 2017, 23:05.
Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos
bdee2fa23401
·Stan Moore on Mar 15 2017, 22:59.
Merge pull request #413 from ohenrich/user-cgdna
3a2da51a8210
·sjplimp / GitHub on Mar 15 2017, 20:12.
Merge pull request #415 from stanmoore1/kk_qeq
b1c59126f750
·sjplimp / GitHub on Mar 15 2017, 20:12.
Merge pull request #414 from sstrong99/flow-gauss-doc-addition
4c77838514d1
·sjplimp / GitHub on Mar 15 2017, 20:11.
Merge pull request #412 from timattox/master_typofix
f9468f46f577
·sjplimp / GitHub on Mar 15 2017, 20:10.
Merge pull request #18 from ibaned/pair-table-rx-kokkos-slow
bd7f4143e292
·Stan Moore / GitHub on Mar 15 2017, 16:47.
pass Views by reference for pair_table_rx_kokkos
f4a08ba4fcae
·Dan Ibanez on Mar 15 2017, 16:25.
Added fix filter/corotate.
c3ce3747e049
·lukin17 on Mar 15 2017, 11:34.

Mar 14 2017

Tweaking docs for Kokkos package
fdc390ad0548
·Stan Moore on Mar 14 2017, 21:08.
Improve the performance of read_data of gzip'ed files using taskset. Normally…
5925460a275f
·Tim Mattox on Mar 14 2017, 20:27.
Add neigh/qeq option to Kokkos
580f6b567b12
·Stan Moore on Mar 14 2017, 17:44.
updated the NEMD discussion in the how-to documentation about flow/gauss
27b1c33a1680
·Steven Strong on Mar 14 2017, 17:39.
Minor updates in documentation and setup tool, merge before upgrade to oxDNA2
7a75cd111c3d
·Oliver Henrich on Mar 14 2017, 12:39.
Updated documentation and simple setup tool
23b828793333
·Oliver Henrich on Mar 14 2017, 12:36.

Mar 13 2017

Add CUDA support to atom_vec_hybrid_kokkos
d2cbfef13bac
·Stan Moore on Mar 13 2017, 16:01.
USER-DPD: specialize PairTableRXKokkos's compute_all_items() on NEWTON_PAIR No…
4b4bc7dc3bd1
·Tim Mattox on Mar 13 2017, 08:03.
USER-DPD Kokkos: add support for full neighbor lists. Note: "newton on" still…
d5eceebf3283
·Tim Mattox on Mar 13 2017, 06:56.

Mar 12 2017

USER-DPD: fix_shardlow's neighbor request needs "newton on" override. Even if…
b1b377cb5947
·Tim Mattox on Mar 12 2017, 22:48.
USER-DPD Kokkos: correct some error messages
e908b8dbea02
·Tim Mattox on Mar 12 2017, 21:20.
USER-DPD: Make newton-off warning in pair_dpd_fdt* be more selective. If using…
d6f6c6faf1ec
·Tim Mattox on Mar 12 2017, 21:05.

Mar 11 2017

Merge branch 'master' into USER-DPD_kokkos as of patch 10 Mar 2017
17c8e695a422
·Tim Mattox on Mar 11 2017, 03:37.
Correct a typo in the fix_halt.txt documentation.
4cfe623bc17d
·Tim Mattox on Mar 11 2017, 03:30.

Mar 10 2017

change to RCB cuts in load-balancing commands, also a new option for fix halt
f871ecdc67db
·Steve Plimpton on Mar 10 2017, 23:55.
Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10
470353e32080
·sjplimp / GitHub on Mar 10 2017, 22:51.
Merge pull request #406 from stanmoore1/kokkos_bugfix
ffe02d20ca83
·sjplimp / GitHub on Mar 10 2017, 22:51.
Merge branch 'master' into USER-DPD_kokkos
c7eadfdefd7f
·Tim Mattox on Mar 10 2017, 22:29.
Include PDF of Colvars doc missing in previous commit
f70752c18f8d
·Giacomo Fiorin on Mar 10 2017, 21:58.
Merge pull request #405 from stanmoore1/ev_setup_kk
07fcfd6d54a1
·sjplimp / GitHub on Mar 10 2017, 19:01.
Merge pull request #407 from frobnitzem/master
c97feafca6ac
·sjplimp / GitHub on Mar 10 2017, 19:00.
Merge pull request #402 from timattox/USER-DPD_spelling
b20d95d49548
·sjplimp / GitHub on Mar 10 2017, 18:59.
Backport typo fixes that were not previously pushed to the Colvars repository
0b4adaa9e6a1
·Giacomo Fiorin on Mar 10 2017, 15:24.
Update Colvars module to version 2017-03-10
5fe620663813
·Giacomo Fiorin on Mar 10 2017, 15:16.

Mar 9 2017

Add Kokkos version of atom_vec_hybrid_kokkos, without CUDA support
6f71275db30f
·Stan Moore on Mar 9 2017, 23:35.
Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp
65964f3b31ea
·David M. Rogers on Mar 9 2017, 22:49.
Fix half from full nlist issue with Kokkos
b28b84d444a4
·Stan Moore on Mar 9 2017, 22:00.
Fixing memory overflow issue in comm_kokkos
a001a5ceb0c4
·Stan Moore on Mar 9 2017, 20:20.

Historymaster20ae05055dbb04054f0c1c6…

Mar 28 2017

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Mar 18 2017

Mar 17 2017

Mar 16 2017

Mar 15 2017

Mar 14 2017

Mar 13 2017

Mar 12 2017

Mar 11 2017

Mar 10 2017

Mar 9 2017

History
master20ae05055dbb04054f0c1c6…