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12201 Commits

Author SHA1 Message Date
Axel Kohlmeyer ce20c7ffe9 remove debug code 2017-02-17 12:42:07 -05:00
Steve Plimpton 4a80df3a99 more neighbor list changes, some new options 2017-02-15 16:45:33 -07:00
Stan Moore 5f93fad012 Add copymode protection to class2 styles 2017-02-15 13:56:16 -07:00
Stan Moore ccaec315db Updating docs for Kokkos class2 2017-02-15 13:00:33 -07:00
Stan Moore c6c1852b3b Fix a few issues with Kokkos class2 files 2017-02-15 12:44:54 -07:00
Stan Moore 69a8e19dc5 Add files from Ray Shan for Kokkos version of class2 angle, bond, etc. 2017-02-15 12:29:52 -07:00
Tim Mattox 928947dcea neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies. 
This corresponds to a bugfix from commit 9161bd98 on neighbor.cpp
 2017-02-15 11:49:34 -05:00
Markus Hoehnerbach 904609a7a3 Fixed issue with switching function derivative in PairAIREBO::FLJ 
Since we compute dvdw as d vdw / d rij, we have to also compute
dslw as d slw / d rij. Currently, we compute -1/r d slw/d rij,
which leads to incorrect results when the two are later combined.
Alternatively, one could also modify dvdw to be -1/r d vdw/d rij,
which would be a more standard way to do LJ calculations, but this
way seems more consistent.
 2017-02-15 16:38:13 +01:00
Markus Hoehnerbach fc3505fac4 Fixed a number of issues after verifying against the KIM version 2017-02-15 16:37:29 +01:00
Axel Kohlmeyer 48070011d9 update names in example, too 2017-02-14 07:42:36 -05:00
Axel Kohlmeyer 0fb8dacc00 one more Finchham to Fincham change 2017-02-14 07:41:05 -05:00
Hendrik Heenen 6b923476b9 updated documentation and examples for coreshell 2017-02-14 13:14:22 +01:00
Trung Nguyen 20806dd86a Fixed bugs with pppm/gpu when used with compute group/group 2017-02-14 00:26:55 -06:00
Stan Moore 90e5ae965d Add missing flags to Kokkos Makefile 2017-02-13 11:19:46 -07:00
Tim Mattox 15008c9d18 USER-DPD: performance optimizations to ssa_update() in fix_shardlow 
Overall improvements range from 2% to 18% on our benchmarks
1) Newton has to be turned on for SSA, so remove those conditionals
2) Rework the math in ssa_update() to eliminate many ops and temporaries
3) Split ssa_update() into two versions, based on DPD vs. DPDE
4) Reorder code in ssa_update_*() to reduce register pressure
 2017-02-13 13:11:19 -05:00
Stan Moore 33af7ab248 Remove merge line 2017-02-13 10:59:22 -07:00
Stan Moore 8f9b2aca06 Removing unused files in Kokkos lib 2017-02-13 10:53:51 -07:00
Stan Moore 383da816c2 Updating Kokkos lib 2017-02-13 10:50:34 -07:00
Markus Hoehnerbach a323ca1edd Moved variable declarations to front for consistency 2017-02-13 18:11:09 +01:00
Markus Hoehnerbach de4af6f15d In PairAIREBO::bondorderLJ correct omega sum d/drij. 
The code tries to make this distinction between the real distance (r23) and the facticious one (rij), but does not do so very well.
It is better if those two variables have the same value everywhere, and apply the correction where necessary.
The current way to use the values is incorrrect.

Remove those calculations that effectively are derivatives w.r.t. |rij| (the facticious distance), is constant and thus the chained derivative (d|rij|/dRij) is always zero.

Apply the corrections due to drij/dRij in the sum omega term.
 2017-02-13 18:11:09 +01:00
Markus Hoehnerbach 0e16dc3ead In PairAIREBO::bondorderLJ: p^sigma pi account for d/drij derivatives. 
The bonderorderLJ function operates on a facticious distance |rij|, i.e. everything gets calculated "as if" atoms i and j were a given distance alpha apart.
Mathematically, bondorderLJ is a function of rij (a vector), that is (in terms of the real distance Rij) rij = alpha * Rij/|Rij|.
When we calculate the forces in bondorderLJ, we have to make sure to chain in this derivative whenever we calculate derivatives w.r.t. rij.
The right correction, as it turns our, is Fij = alpha / |Rij| * (Identity(3,3) - Rij * Rij^T / |Rij|^2) * fij.
This commit only fixes this for the p_ij^sigma pi terms, which were modified to separate out the d/drij derivative in the cosine calculation.
Now, derivatives are taken w.r.t. the connecting edges instead of the edge points.
 2017-02-13 18:11:01 +01:00
Markus Hoehnerbach 1b3f6e257a In PairAIREBO::bondorderLJ only compute torsion term once. 
Since Etmp (representing sum_kijl omega_kijl * w_ik * w_jl) is not reset between the forward and reverse pass, the value used by later calculation will be twice the expected values.
One could instead reset Etmp between these passes, but there really is no reason to calculate it twice.
 2017-02-13 17:14:52 +01:00
Steve Plimpton cb982f2f28 sync 13Feb17 patch back to GH 2017-02-13 09:05:03 -07:00
sjplimp 4843296d4e Merge pull request #372 from akohlmey/fft-cleanup 
simplify FFT3d code by removing support for outdated FFT libraries
 2017-02-13 08:53:13 -07:00
Steve Plimpton 2bdda8f6c0 patch 12Feb17 - change int to tagint for compute group/group 2017-02-13 08:40:54 -07:00
Steve Plimpton 0068ef5616 added molecule option to compute group/group command 2017-02-10 09:25:32 -07:00
sjplimp 02b0e6cc55 Merge pull request #375 from akohlmey/small-updates-and-fixes 
Small updates and fixes
 2017-02-10 09:23:51 -07:00
sjplimp fbb24c2406 Merge pull request #374 from agiliopadua/master 
Updated polarizer.py in USER-DRUDE to use coul/long/cs
 2017-02-10 09:22:22 -07:00
Oliver Henrich 0efd209480 Merge branch 'master' into user-cgdna 2017-02-09 11:50:03 +00:00
Axel Kohlmeyer a5f830c40c fix typo 
(cherry picked from commit 6410797697)
 2017-02-08 14:33:45 -05:00
Axel Kohlmeyer 8c074a363a Merge branch 'master' into small-updates-and-fixes 2017-02-08 14:32:44 -05:00
Agilio Padua 27aca14094 Updated polarizer.py to use coul/long/cs 2017-02-04 15:02:08 +01:00
Axel Kohlmeyer 191453e1c7 Merge branch 'master' into fft-cleanup 2017-02-03 16:53:10 -05:00
sjplimp 207adc3968 Merge pull request #373 from stanmoore1/kk_more_bugfixes 
Fixing Kokkos per-atom energy/virial issues
 2017-02-03 14:45:31 -07:00
sjplimp 84c517159d Merge pull request #368 from Pakketeretet2/kokkos_morse 
Kokkos morse
 2017-02-03 14:45:07 -07:00
sjplimp 6ca377436f Merge pull request #366 from rbberger/kokkos_lammps_bigbig_fix 
Fix data type of molecule array in npair_kokkos.h
 2017-02-03 14:43:33 -07:00
sjplimp dc34a32602 Merge pull request #362 from ibaned/warnings2 
fix Kokkos+kspace warnings
 2017-02-03 14:43:12 -07:00
Stan Moore 067119f6c6 Adding missing friend statement to pair_lj_class2_coul_cut_kokkos 2017-02-02 15:21:30 -07:00
Stan Moore 1834a5e46c Fixing more Kokkos per-atom and fdotr issues 2017-02-02 15:21:21 -07:00
Stan Moore 6a4918b39a Fixing typo in pair_buck_coul_cut_kokkos 2017-02-02 15:21:05 -07:00
Stan Moore 5da0d39392 Fixing fdotr in pair_buck_coul_cut_kokkos 2017-02-02 13:35:51 -07:00
Stan Moore 6f92429602 Fixing per-atom ev issue 2017-02-02 13:34:27 -07:00
Stan Moore 38e0e4bb69 Add missing typedef in Kokkos pair styles 2017-02-02 13:24:05 -07:00
Stan Moore daf9f95381 Fixing Kokkos per-atom e/v issue 2017-02-02 13:09:52 -07:00
Axel Kohlmeyer 6595fde0a1 explain in more detail the handling of error checking for numerical inputs 2017-02-02 11:58:12 -05:00
Richard Berger 6bcec9c61d Merge pull request #2 from stanmoore1/kk_tag_bugfixes 
Fixing tagint and imageint issues in Kokkos package
 2017-02-02 08:57:21 -05:00
Axel Kohlmeyer 9d1991bf84 remove support for obsolete legacy FFT libraries and point -DFFT_FFTW to FFTW3 2017-02-02 08:10:23 -05:00
Stefan Paquay 0a87b7443a Updated contributing authors and docs 2017-02-02 13:42:47 +01:00
Stan Moore 7ee45ec5f3 Fixing tagint and imageint issues in Kokkos package 2017-02-01 11:52:27 -07:00
Stefan Paquay d4c9e2500b Ported Morse to KOKKOS 2017-02-01 17:45:21 +01:00