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6898 Commits

Author SHA1 Message Date
Steve Plimpton f871ecdc67 change to RCB cuts in load-balancing commands, also a new option for fix halt 2017-03-10 15:55:07 -07:00
sjplimp 470353e320 Merge pull request #408 from giacomofiorin/colvars-update-2017-03-10 
Colvars update 2017-03-10
 2017-03-10 14:51:16 -07:00
sjplimp ffe02d20ca Merge pull request #406 from stanmoore1/kokkos_bugfix 
Fix Kokkos issues
 2017-03-10 14:51:04 -07:00
sjplimp 07fcfd6d54 Merge pull request #405 from stanmoore1/ev_setup_kk 
Add alloc flag to ev_setup
 2017-03-10 11:01:51 -07:00
sjplimp c97feafca6 Merge pull request #407 from frobnitzem/master 
Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp
 2017-03-10 11:00:30 -07:00
Giacomo Fiorin 5fe6206638 Update Colvars module to version 2017-03-10 2017-03-10 09:16:58 -05:00
David M. Rogers 65964f3b31 Add error check to lammps_gather_atoms/lammps_scatter_atoms in library.cpp 2017-03-09 16:49:07 -05:00
Stan Moore b28b84d444 Fix half from full nlist issue with Kokkos 2017-03-09 14:00:27 -07:00
Stan Moore a001a5ceb0 Fixing memory overflow issue in comm_kokkos 2017-03-09 12:20:49 -07:00
Axel Kohlmeyer 2ef713ea1b restore incorrect change due to spell checking in fix imd 2017-03-08 16:40:16 -05:00
Stan Moore 1f6c1942b3 Disable allocation of per-atom arrays in ev_setup for Kokkos styles 2017-03-08 12:42:44 -07:00
Stan Moore 683023d820 Adding alloc flag to ev_setup 2017-03-08 12:36:23 -07:00
Tim Mattox 42d3a8f498 Fix spelling "correction" from 3a054d1a: iterations not interactions. :-) 2017-03-07 15:41:06 -05:00
Steve Plimpton 79b005dc3d patch 7Mar17 2017-03-07 11:40:07 -07:00
sjplimp a2fa6ef452 Merge pull request #393 from akohlmey/small-bugfixes 
Small bugfixes
 2017-03-07 09:56:03 -07:00
sjplimp 920641bbff Merge pull request #399 from rbberger/docs_spelling_fixes 
Correct spelling errors in documentation
 2017-03-07 09:47:22 -07:00
sjplimp c2aabdec22 Merge pull request #398 from stanmoore1/kokkos_changes 
Kokkos changes
 2017-03-07 09:46:54 -07:00
sjplimp e4aa735a68 Merge pull request #395 from timattox/USER-DPD_bugfix 
USER-DPD: a variety of small but important bugfixes
 2017-03-07 09:46:40 -07:00
sjplimp 4af6557568 Merge pull request #394 from jaapkroe/kolmogorov-crespi 
Added Kolmogorov-Crespi potential
 2017-03-07 09:46:08 -07:00
sjplimp 0798885bdb Merge pull request #389 from akohlmey/update-agni-potential 
update AGNI potential for Al, reference runs and output and citation
 2017-03-07 09:35:31 -07:00
sjplimp d6866f1cfd Merge pull request #376 from v0i0/airebo-bondorderLJ-fixes 
Fixes for PairAIREBO::bondorderLJ
 2017-03-07 09:32:30 -07:00
Steve Plimpton efaa4c6710 new neigh_modify exclude option, other SNAP changes 2017-03-07 09:31:12 -07:00
Richard Berger 3a054d1a82 Fix more typos in src files 2017-03-07 00:55:01 -05:00
Richard Berger 7dd60f9737 Fix typos in src files 2017-03-05 21:03:40 -05:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Stan Moore 6382d3c89a Improving memory access in comm_kokkos 2017-03-03 09:14:47 -07:00
Tim Mattox 763a00e8b0 USER-DPD: pair_multi_lucy_rx bugfix for systems with multiple atom types 2017-03-03 09:29:17 -05:00
Axel Kohlmeyer ce1a3f25e1 Merge branch 'pair_write_fix' of https://github.com/andeplane/lammps into small-bugfixes 2017-03-03 08:11:55 -05:00
Anders Hafreager eaf7ed7707 Print error if pair_write does not get correct number of arguments 2017-03-02 21:25:27 -08:00
Tim Mattox 9a560b9091 USER-DPD bugfix: make atom_vec_dpd work properly with atom_vec_hybrid. 
We were sending too much data during pack_comm_hybrid/unpack_comm_hybrid.
 2017-03-01 15:22:28 -05:00
Jaap Kroes 8a0e44db83 updated documentation and ev_tally 2017-03-01 16:13:44 +01:00
Tim Mattox 1dc78a7e58 USER-DPD: correct off-by-one errors in PairMultiLucyRX::coeff() 2017-02-28 17:45:21 -05:00
Tim Mattox 7a593c2fc8 USER-DPD: correct off-by-one errors in PairTableRX::coeff() 2017-02-28 14:25:03 -05:00
Axel Kohlmeyer 3605208a45 add a few more missing details for integrating pair style kolmogorov/crespi/z 2017-02-28 11:16:27 -05:00
Jaap Kroes 323570c920 added jpg for kolmogorov-crespi-z equations and fixed hybrid/overlay check in source 2017-02-28 15:39:01 +01:00
Jaap Kroes df13a7a003 email added 2017-02-28 15:12:35 +01:00
Jaap Kroes a1b40b902d Added Kolmogorov-Crespi potential 2017-02-28 14:59:13 +01:00
Axel Kohlmeyer b921b69f47 implement bugfix from issue #388 
this closes #388
 2017-02-27 18:22:21 -05:00
Axel Kohlmeyer c0cf50bce5 trigger recomputing ichunk between runs unless requested otherwise 
this fixes #390
 2017-02-27 18:19:59 -05:00
Axel Kohlmeyer a18b4ef4b0 update AGNI potential for Al, reference runs and output and citation 2017-02-24 15:33:13 -05:00
Oliver Henrich 3626496c7c Corrected comment in 3' to 5' directionality check 2017-02-22 20:06:49 +00:00
Steve Plimpton 49e83b4348 patch 21Feb17 sync with GHub 2017-02-21 16:07:26 -07:00
sjplimp 6e89ccd522 Merge pull request #385 from akohlmey/collected-small-bugfixes 
collected small bugfixes and updates
 2017-02-21 15:59:06 -07:00
Steve Plimpton 3dbbea342a remove a debug print line 2017-02-21 15:57:03 -07:00
sjplimp b70c670aac Merge pull request #383 from stanmoore1/rshan_class2_kk 
Kokkos version of class2 bond, angle, dihedral, and improper from Ray Shan
 2017-02-21 15:52:10 -07:00
sjplimp 1d17cae407 Merge pull request #382 from timattox/master_kokkos_neigh_bugfix 
neighbor_kokkos.cpp: Don't call grow() on neighbor lists that are copies
 2017-02-21 15:51:35 -07:00
sjplimp d001a09345 Merge pull request #379 from ndtrung81/pppm-gpu-compute-group-group 
Fixed bugs with pppm/gpu when used with compute group/group
 2017-02-21 15:50:28 -07:00
sjplimp cb9d42da08 Merge pull request #378 from timattox/USER-DPD_ssa_update 
USER-DPD: performance optimizations to ssa_update() in fix_shardlow
 2017-02-21 15:50:07 -07:00
Steve Plimpton 1cd4c48ccc new SNAP potential for W 2017-02-21 15:49:21 -07:00
Axel Kohlmeyer a88136c3f5 correct a logic bug in fix wall/gran/region 2017-02-17 17:58:24 -05:00
Stan Moore 5f93fad012 Add copymode protection to class2 styles 2017-02-15 13:56:16 -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
Trung Nguyen 20806dd86a Fixed bugs with pppm/gpu when used with compute group/group 2017-02-14 00:26:55 -06:00
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
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
Axel Kohlmeyer a5f830c40c fix typo 
(cherry picked from commit 6410797697)
 2017-02-08 14:33:45 -05:00
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
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
Stefan Paquay 6232073d3b Removed traces of pair morse/kk 2017-02-01 17:39:37 +01:00
Stefan Paquay ed59193d13 Removed traces of pair morse/kk 2017-02-01 17:39:06 +01:00
Axel Kohlmeyer bcb1d94b9a silence compiler warning about dead code 2017-01-31 18:28:04 -05:00
Axel Kohlmeyer fbe30b5683 correct issue with compiling for -DLAMMPS_BIGBIG in fix qeq/reax/kk 2017-01-31 18:13:44 -05:00
Axel Kohlmeyer 9ef55fedf7 Merge branch 'kokkos_lammps_bigbig_fix' of https://github.com/rbberger/lammps into tagint-issue 2017-01-31 17:23:51 -05:00
sjplimp 997142a4c1 Merge pull request #364 from stanmoore1/kk_triclinic_neighlist 
Add triclinic neighbor list support to Kokkos
 2017-01-30 07:27:02 -07:00
Richard Berger 51a0b6b445 Fix data type of molecule array in npair_kokkos.h 
This showed up when trying to compile with -DLAMMPS_BIGBIG.
Fixes issue #365
 2017-01-28 07:49:08 -05:00
Stan Moore 59f4a77dd5 Whitespace change to npair_kokkos 2017-01-27 15:17:39 -07:00
Stan Moore 579cc6d7aa More tweaks to npair_kokkos for triclinic 2017-01-27 15:13:37 -07:00
Stan Moore 5afd3e995b Adding support to npair_kokkos for triclinic-newton-on neighborlists 2017-01-27 14:18:01 -07:00
Dan Ibanez 2a6f5e651c more preference of datamask over custom sync 
see commit 09fc8b0 for details on why
 2017-01-27 09:35:55 -07:00
Dan Ibanez 09fc8b0bd7 kspace & dihedral can't do their own sync/modify 
because the verlet_kokkos system has
a "clever" optimization which will
alter the datamasks before calling sync/modify,
so the datamask framework must be
strictly obeyed for GPU correctness.
(the optimization is to concurrently
compute forces on the host and GPU,
and add them up at the end of an iteration.
calling your own sync will overwrite
the partial GPU forces with the
partial host forces).
 2017-01-27 08:39:55 -07:00
Dan Ibanez e5d0bde783 pppm_kokkos: remove useless statement 2017-01-27 08:35:37 -07:00
Dan Ibanez 9daf7fb650 pppm_kokkos: don't shadow member variables 2017-01-27 08:35:37 -07:00
Dan Ibanez b5d622c6a3 pppm_kokkos: remove unused variables 2017-01-27 08:35:37 -07:00
Dan Ibanez 2023fa28e0 consistent #ifdefs for fft3d variable (2) 
this variable is only used when FFTW3
is enabled, so its declaration and
initialization should be protected
under the same conditions to avoid
compiler warnings
 2017-01-27 08:35:37 -07:00
Dan Ibanez 5b29515849 fft3d: use C++ loop declarations 
the variable (offset) is only
used in a subset of numerous
scenarios with #ifdef, it seems
better just to have each loop
declare it as needed.
(avoids compiler warnings)
 2017-01-27 08:35:37 -07:00
Dan Ibanez 5b18421dd2 fft3d : remove unused variables 2017-01-27 08:35:37 -07:00
Dan Ibanez cf95ea0709 fft3d: only declare variables when used 
avoids compiler warnings
 2017-01-27 08:35:36 -07:00
Dan Ibanez 6a74a81da0 consistent #ifdefs for fft3d variable 
this variable is only used when FFTW3
is enabled, so its declaration and
initialization should be protected
under the same conditions to avoid
compiler warnings
 2017-01-27 08:35:36 -07:00
Dan Ibanez f0a4ed615d add missing KOKKOS_INLINE_FUNCTION for params 2017-01-27 08:35:36 -07:00
Dan Ibanez cfe818a175 remove unused variables from fix_cmap 2017-01-27 08:35:36 -07:00
Steve Plimpton f8506fee23 sync GHub with SVN 2017-01-26 14:06:43 -07:00
sjplimp 18e5584311 Merge pull request #354 from stanmoore1/kokkos_bugfixes 
Kokkos bugfixes
 2017-01-26 13:51:47 -07:00
sjplimp 851f80464f Merge pull request #361 from akohlmey/user-omp-fix-per-atom-data 
fix USER-OMP bug on per-atom data with hybrid styles
 2017-01-26 13:50:13 -07:00
sjplimp 5971d4c994 Merge pull request #358 from ibaned/warnings 
warning fixes (Kokkos+CUDA)
 2017-01-26 13:49:56 -07:00
sjplimp 868d95f0a5 Merge pull request #352 from akohlmey/fix-skip-with-ghost-issue 
Fix skip with ghost issue
 2017-01-26 13:47:12 -07:00
Axel Kohlmeyer 8b7bd9d88e fix bug where per atom data for USER-OMP was reducing the wrong arrays with hybrid styles 2017-01-26 14:59:10 -05:00
Dan Ibanez 672bbbe494 add more missing KOKKOS_INLINE_FUNCTION attributes 2017-01-25 16:03:11 -07:00
Dan Ibanez 03c9c46533 add missing KOKKOS_INLINE_FUNCTION attributes 2017-01-25 15:49:05 -07:00
Dan Ibanez e992bfe510 remove unused variable 2017-01-25 15:40:52 -07:00
Dan Ibanez 053ee54a27 remove unused variable 2017-01-25 15:38:41 -07:00
Dan Ibanez 1074c6734b add missing return keywords 2017-01-25 15:37:27 -07:00
Dan Ibanez 60b48c9d66 add missing KOKKOS_INLINE_FUNCTION attributes 
this structure gets put inside a DualView,
so these members need to be able to execute
on the GPU
 2017-01-25 15:36:24 -07:00
Dan Ibanez 3d40b51708 remove unused variable 2017-01-25 15:24:52 -07:00
Dan Ibanez effbe18c46 fix domain boundary indexing 
the compiler pointed out that
boundary[2][2] doesn't exist.
If I understand this correctly,
those checks should be against
boundary[*][0].
 2017-01-25 15:24:01 -07:00
Dan Ibanez 6328beb7d7 fix double-return warning 
this #ifdef adds a return statement
for little endian machines, but leaves
the old one, which the compiler comlains
is unreachable. this commit combines
the conditionals so we can use #else
 2017-01-25 15:22:42 -07:00
Stan Moore 26c8d3d98f Fixing GPU memory issue in fix_langevin_kokkos 2017-01-25 12:53:55 -07:00
Stan Moore 73177d650d Fixing GPU memory issue in domain_kokkos 2017-01-25 11:18:03 -07:00
Axel Kohlmeyer b5cb74bd33 skip list build is compatible with NP_GHOST 2017-01-23 19:21:48 -05:00
Axel Kohlmeyer 31976d1dee skip list definition was missing NP_HALFFULL flag 2017-01-23 19:20:05 -05:00
Christopher Stone c8260af37c Possible uninitialized variable in USER-DPD/pair_exp6_rx.cpp bugfix. 
Added explicit initialization (to zero) for several variables inside the
inner j-loop to avoid using them uninitialized or from prior iterations
within rmOldij_12 == 0.
 2017-01-23 13:34:51 -05:00
Steve Plimpton caea8973a3 add neighbor list kind output to screen 2017-01-20 13:24:09 -07:00
sjplimp aa0ad9b483 Merge pull request #349 from akohlmey/collected-small-fixes 
collected fixes and improvements
 2017-01-20 13:19:43 -07:00
sjplimp 5d0e4e1ba9 Merge pull request #346 from stanmoore1/kokkos_fixes 
Kokkos fixes
 2017-01-20 13:15:16 -07:00
sjplimp f8d3c4c740 Merge pull request #345 from timattox/USER-DPD_another_zero_compute 
USER-DPD another zero compute optimization
 2017-01-20 13:14:59 -07:00
Axel Kohlmeyer e6996121d1 remove dead code 2017-01-20 14:30:46 -05:00
Axel Kohlmeyer fbfb1df5eb fix typo causing wrong neighbor list copy selections 2017-01-19 20:47:10 -05:00
Steve Plimpton 9a299875da simplified neighbor list copying to avoid possible same-timestep re-build issues 2017-01-19 17:01:15 -07:00
Stan Moore fc94f1bd18 Fixing GPU memory issues in Kokkos 2017-01-19 12:14:25 -07:00
Stan Moore 5ce8e2fbae Fixing GPU memory issue in modify_kokkos, need to cherry pick back to Master 2017-01-19 12:13:48 -07:00
Tim Mattox f6cd98636b USER-DPD: Also apply "check if a0 is zero" optimization to pair_dpd_fdt 
This relates to commit 4eb08a5822 that was applied to pair_dpd_fdt_energy
 2017-01-18 16:17:11 -05:00
Tim Mattox 05cafb716f USER-DPD: cleanup initialization of splitFDT_flag in pair_dpd_fdt.cpp 2017-01-18 15:51:50 -05:00
sjplimp 3af4b3c28c Merge pull request #337 from ohenrich/user-cgdna 
Added source code and documentation for USER-CGDNA
 2017-01-18 11:31:35 -07:00
sjplimp 7fc0970587 Merge pull request #344 from timattox/USER-DPD_zero_compute 
USER-DPD: Skip a0*stuff computations, if a0 was set to zero in pair_coeff
 2017-01-18 11:31:14 -07:00
Tim Mattox 4eb08a5822 USER-DPD: Skip a0*stuff computations, if a0 was set to zero in pair_coeff. 
This saves around 10% of the runtime for many of our tests using SSA.
 2017-01-17 15:55:39 -05:00
Tim Mattox 01609f55e2 USER-DPD: bugfix for a segfault when using MOLECULE and DPD together. 2017-01-17 12:47:59 -05:00
Steve Plimpton d2fc88a626 patch 17Jan17 2017-01-17 10:14:53 -07:00
sjplimp c52a26382f Merge pull request #339 from akohlmey/fixes-for-srp-example 
Fixes for srp example
 2017-01-17 09:36:28 -07:00
sjplimp ad4d299975 Merge pull request #335 from stanmoore1/neighbor_fixes 
Neighbor fixes
 2017-01-17 09:33:25 -07:00
sjplimp 83408b195f Merge pull request #342 from epfl-cosmo/ipi-multiinit-bug 
Bugfix in the fix_ipi initialization - prevents multiple open_socket calls
 2017-01-17 09:14:03 -07:00
sjplimp cd7bdf9251 Merge pull request #341 from stanmoore1/qeq_kk_neighlist 
Make fix_qeq_reax_kokkos request its own neighbor list
 2017-01-17 09:13:47 -07:00
sjplimp 8c5b108900 Merge pull request #340 from stanmoore1/fix_rx_neighborlist 
Make fix_rx request its own neighbor list
 2017-01-17 09:13:27 -07:00
sjplimp c19d2011bb Merge pull request #334 from sstrong99/flow_gauss_changeRef 
Updated the reference for the flow/gauss method
 2017-01-17 09:12:22 -07:00
sjplimp 973bef4d45 Merge pull request #332 from akohlmey/coord-atom-orientorder-atom-enhancements 
Coord atom orientorder atom enhancements
 2017-01-17 09:11:45 -07:00
sjplimp 252e07e083 Merge pull request #330 from akohlmey/collected-small-bugfixes 
Collected small bugfixes
 2017-01-17 09:08:00 -07:00
sjplimp 74a661ae26 Merge pull request #328 from akohlmey/print-last-command-on-error 
print the last input line, when error->all() is called
 2017-01-17 09:05:19 -07:00
sjplimp d8bc590aaf Merge pull request #327 from stanmoore1/kokkos_lib_update 
Updating Kokkos lib
 2017-01-17 09:04:12 -07:00
Steve Plimpton 5cd856c97f fix spring doc page update 2017-01-17 09:02:56 -07:00
Axel Kohlmeyer 2f13365cf5 avoid spurious error message, when no storage fix is active/used 2017-01-16 17:08:00 -05:00
Axel Kohlmeyer 0a2b78acb8 rather than adjusting the communication cutoff, we just print out the minimum value needed and error out 
i suspect, this communication cutoff adjustment was included into the code before it was possible to separately set it via comm_modify. stopping with an error message printing the needed/current value is cleaner, in keeping with other modules in LAMMPS and much less problematic.
 2017-01-16 15:47:02 -05:00
Axel Kohlmeyer 3f46b6d782 fix bugs from incorrect code synchronization 2017-01-16 11:15:54 -05:00
Axel Kohlmeyer 5abd6e5122 reordering operations in Pair::init_style() to avoid segfaults w/o a kspace style 2017-01-16 11:08:48 -05:00
Michele Ceriotti f3a82f454e Included a flag to prevent multiple open_socket calls if run is included multiple times in the LAMMPS input 2017-01-16 08:42:23 +01:00
Axel Kohlmeyer 473a3ebeef fix for bug with compute rdf with pair reax/c. we must not copy a neighbor list, if newton settings are not compatible 
an alternate route to address this issue would be to allow an "ANY" setting for neighbor list requests and then query the neighbor list for newton setting instead of the force class.
 2017-01-15 12:05:19 -05:00
Stan Gerald Moore (stamoor) b220850377 Removing neighbor list hack in fix_qeq_reax_kokkos 2017-01-14 16:16:02 -07:00
Stan Gerald Moore (stamoor) fa00e0593f Make fix_rx request its own neighbor list 2017-01-14 15:39:37 -07:00
Axel Kohlmeyer 4a09399dc6 during setup, checking timestep doesn't seem to be sufficient. comparing bins and stencil point, too. 
in addition, relevant pointers were not properly initialized to NULL
 2017-01-14 17:13:22 -05:00
Axel Kohlmeyer 5821fe8dd5 correct out-of-bounds accesses 2017-01-14 17:06:23 -05:00
Axel Kohlmeyer b988b29413 remove dead code 2017-01-13 18:43:35 -05:00
Axel Kohlmeyer 5d48bfdcab USER-CGDNA whitespace cleanup: expand tabs and remove trailing whitespace 2017-01-13 18:40:34 -05:00
Axel Kohlmeyer fe8caa8a56 apply some LAMMPS formatting style conventions for include files 2017-01-13 18:33:32 -05:00
Axel Kohlmeyer afaacc6173 add USER-CGDNA package with dependencies into the build system 2017-01-13 18:32:32 -05:00
Axel Kohlmeyer 61cff85435 avoid not only division by zero, but also computing variance for short runs with insufficient resolution 2017-01-13 14:35:35 -05:00
Axel Kohlmeyer aa0b327f7e Merge branch 'bugfix_dividebyzero' of https://github.com/timattox/lammps_USER-DPD into collected-small-bugfixes 2017-01-13 14:26:10 -05:00
Tim Mattox 78498715b4 Protect from divide by zero in mpi_timings() when printing results. 
e.g. If neighbor list(s) are never rebuilt, the Neigh time will be zero.
 2017-01-13 13:32:15 -05:00
Oliver Henrich 96259ea2d2 Added source code and documentation for USER-CGDNA 2017-01-13 13:36:54 +00:00
Axel Kohlmeyer b2f67fea30 Merge branch 'collected-small-bugfixes' of github.com:akohlmey/lammps into collected-small-bugfixes 2017-01-13 08:12:10 -05:00
Axel Kohlmeyer c59bcf31d1 change $MKLROOT to $(MKLROOT) as reported by @WeiLiPenguin 
This closes #336
 2017-01-13 08:10:51 -05:00
Axel Kohlmeyer e8e03dd440 Updated the reference for the flow/gauss method, the new reference is much more comprehensive 2017-01-12 23:44:33 -05:00
Stan Moore daf766d4f8 Fixing Kokkos neighbor bug 2017-01-12 16:22:38 -07:00
Stan Moore 630783c8e8 Fixing neighbor bug 2017-01-12 16:22:24 -07:00
Dan Ibanez c94030d966 put pair_lj_coul in kokkos_type.h 
also rename pair_lj_coul_gromacs
so it doesn't conflict with the
one now in kokkos_type.h
 2017-01-12 13:37:53 -07:00
Axel Kohlmeyer 0b081b0086 whitespace cleanup 2017-01-11 21:05:32 -05:00
Axel Kohlmeyer 8e1cf6643c apply bugfix to fix wall/gran by eric_lyster@agilent.com on lammps-users 2017-01-11 20:59:40 -05:00
Dan Ibanez 9f4e5e0661 fix a CUDA constructor warning 
The class params_lj_coul was copy-pasted
into many different pair styles, and only
one of them had the proper KOKKOS_INLINE_FUNCTION
annotations for CUDA.
created a header file for this class that
most of the pair styles now include.
One pair style did add extra members,
so it keeps a local copy of the class.
 2017-01-11 09:11:35 -07:00
Stan Moore 7839c335da Fixing compile error with Kokkos CUDA Makefiles 2017-01-10 13:05:00 -07:00
Axel Kohlmeyer 92d15d4a89 replace string compare with enums, fix memory leak, formatting cleanup 2017-01-10 12:52:37 -05:00
Axel Kohlmeyer 95706ac846 import contributed code for computes coord/atom and orientorder/atom 2017-01-10 12:29:22 -05:00
Axel Kohlmeyer d014e00e53 ignore some newly added styles from packages. 2017-01-09 17:51:38 -05:00
Axel Kohlmeyer e5ac49d1de Merge branch 'master' into collected-small-bugfixes 2017-01-09 17:13:46 -05:00
Axel Kohlmeyer 1a81da0f73 print the last input line, when error->all() is called 
this should help tracking down input file errors for many
common cases without having to repeat the run with -echo screen
and avoid having to explain how to use that feature all the time
 2017-01-09 17:03:06 -05:00
Steve Plimpton c31f1e9f22 add fix mscg command, example, lib 2017-01-09 13:36:40 -07:00
Stan Moore 9250a55923 Adding enable_lambda to KOKKOS_CUDA_OPTIONS 2017-01-09 12:24:30 -07:00
Axel Kohlmeyer 09af780aa8 remove misleading comments 2017-01-06 21:31:39 -05:00
Steve Plimpton 51fa33a407 patch 6Jan17 2017-01-06 11:14:48 -07:00
Steve Plimpton 142770cb2a enable pppm/tip4p to work with triclinic 2017-01-06 10:38:32 -07:00
sjplimp 63f202501b Merge pull request #324 from ibaned/pair-table-kokkos-inherit 
get PairTableKokkos to inherit from PairTable (also fix GPU)
 2017-01-06 10:10:59 -07:00
sjplimp 83da5d3b5d Merge pull request #323 from akohlmey/pppm-cg-triclinic 
synchronize pppm/cg with changes in pppm and remove block on triclinic
 2017-01-06 10:10:09 -07:00
sjplimp ebbf60b112 Merge pull request #319 from andeplane/domain_bug 
Fixed bug in lamda_box_corners function
 2017-01-06 10:03:32 -07:00
sjplimp 12c4fa25e8 Merge pull request #318 from andeplane/initialize_pointers 
Initializing pointers in neighbor.cpp
 2017-01-06 10:03:05 -07:00
sjplimp 3ac58452de Merge pull request #310 from EfremBraun/master 
Fix nvk implemented
 2017-01-06 10:02:22 -07:00
sjplimp 467377094a Merge pull request #314 from stanmoore1/fix-momentum-kokkos 
Fix momentum kokkos
 2017-01-06 10:01:17 -07:00
sjplimp 5656e90b78 Merge pull request #313 from stanmoore1/kokkos_bugfixes 
Kokkos bugfixes
 2017-01-06 10:00:33 -07:00
sjplimp 41a6a3076e Merge pull request #309 from giacomofiorin/colvars-2016-12-22 
Update Colvars library to version 2016-12-22
 2017-01-06 09:58:20 -07:00
sjplimp d4e8d47387 Merge pull request #306 from timattox/USER-DPD_updates 
USER-DPD updates
 2017-01-06 09:58:01 -07:00
Steve Plimpton f6a819580c pair TIP4P bug fix for cutoffs >> box size 2017-01-06 09:57:27 -07:00
Dan Ibanez 9bf771207d make PairTable::allocate() virtual 
forgot to extract this change when
separating the commits for PairTableRX
and PairTableKokkos.
 2017-01-05 20:46:05 -07:00
Dan Ibanez b9144d6332 Revert "move enum to pair.h" 
This reverts commit aebc8ea826.
 2017-01-05 20:22:15 -07:00
Dan Ibanez 267f05e5ca protect PairTable dtor with copymode 2017-01-05 15:38:45 -07:00
Dan Ibanez aebc8ea826 move enum to pair.h 
to avoid having it be replicated
in several different locations
 2017-01-05 15:38:45 -07:00
Dan Ibanez 53a1de1d40 fix several GPU memory bugs in pair_table_kokkos 2017-01-05 15:38:45 -07:00
Dan Ibanez d059b5d334 fix crash in create_kokkos_tables 
the code was crashing when trying to
deep_copy or assign views that had
not been allocated
 2017-01-05 15:38:45 -07:00
Dan Ibanez 7cff343680 fix allocation regressions in PairTableKokkos 2017-01-05 15:38:45 -07:00
Dan Ibanez a1ac861084 PairTableKokkos : public PairTable 2017-01-05 15:38:45 -07:00
Dan Ibanez 17bdb57bb4 try PairTableKokkos : public PairTable 
realize that there is a lot of copy-paste
in this codebase.
 2017-01-05 15:38:45 -07:00
Dan Ibanez 4cfe122ac6 fix warning about enum comparisons 2017-01-04 08:10:08 -07:00
Stan Moore b46629ee39 Merge pull request #5 from ibaned/kokkos-fixes 
prevent implicit dereference of s_CTEMP
 2017-01-04 08:06:55 -07:00
Anders Hafreager 42bbeb3f16 NULLing pointers after delete 2017-01-04 16:04:05 +01:00
Dan Ibanez a7c5905ca4 prevent implicit dereference of s_CTEMP 2017-01-03 15:17:33 -07:00
Anders Hafreager 37d5567f6d Fixed bug in lamda_box_corners function 2017-01-03 11:54:14 +01:00
Anders Hafreager b10d0c17ec Initializing pointers in neighbor.cpp 2017-01-03 11:24:48 +01:00
Axel Kohlmeyer 94c4f8fe5f add authorship attribution 2016-12-28 17:03:37 -05:00
Efrem Braun aa146e9b38 Moved fix_nvk to USER-MISC, updated documentation to reflect move 2016-12-28 19:06:35 +01:00
Stan Moore eca9539f84 Disallowing full neighborlist for pair_tersoff_kokkos styles until a bugfix is released 2016-12-28 10:59:53 -07:00
Stan Moore 27172c4a55 Fixing Kokkos bug when many atom types 2016-12-28 10:59:42 -07:00
Stan Moore 4f195254af Fixing bug with Kokkos and reading restart files 2016-12-28 10:59:30 -07:00
Dan Ibanez 9a0007a13f rename region_block_kokkos inside() 
this prevents compiler confusion with
the inside() function provided by
the normal region_block, as the two
should be completely separate.
 2016-12-28 10:56:16 -07:00
Dan Ibanez 994f36bc6f silence "implicit dereference" warning 
see kokkos/kokkos#177 for detailed
discussion of the issue and fix
 2016-12-28 10:56:06 -07:00
Dan Ibanez b3557bfbf5 add missing return in comm_tiled_kokkos 2016-12-28 10:55:51 -07:00
Dan Ibanez 371df8ea72 repair sync bugs in fix_momentum_kokkos 
Since the Group class is completely
unaware of Kokkos, the direct calls from
FixMomentumKokkos to Group methods
need to be preceded by atomKK->sync calls
for every atom variable that Group intends
to use.
fix_momentum_kokkos definitely does not
work on GPUs prior to this commit.
 2016-12-28 10:51:59 -07:00
Dan Ibanez 06ae2804f6 ensure velocity is marked as modified before syncing 
it worked before, but this seems more reliable
 2016-12-28 10:51:20 -07:00
Efrem Braun 68814d4fc8 Made documentation changes to fix nvk 2016-12-28 16:26:05 +01:00
Efrem Braun 616ca1de03 Fix nvk implemented. 2016-12-28 16:17:07 +01:00
Giacomo Fiorin f553e230db Update Colvars library to version 2016-12-22 
Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
 2016-12-27 13:17:34 -05:00
Axel Kohlmeyer 634eb357d2 synchronize pppm/cg with pppm and remove block on triclinic 2016-12-24 16:09:18 -05:00
Tim Mattox a1036f2d74 USER-DPD: bugfix for new PairExp6rx::polynomialScaling() function. 2016-12-23 11:36:59 -05:00
Tim Mattox 3faa57a413 USER-DPD: Several updates to *_rx files: 
1) Added MY_EPSILON to handle machine precision checks
2) Removed error checks for DPD-RX; enabled use with DPD-E simulations
3) Expanded the EOS functional form to allow corrections
   in the thermo file or on the command line
4) Updated naming convention from fraction to mixWtSite*
5) Changed the name of getParams() method to getMixingWeights()
6) getMixingWeights() now handles fractional and molecular weighting
7) Added optional argument (fractional or molecular) to pair_style command
8) Added argument to specify the exp6 parameter scaling method
   NOTE: Requires additional arguments in the pair coefficients,
   thus command line areguments are NOT backward-compatible.
 2016-12-22 17:15:09 -05:00
Tim Mattox fa435fb514 USER-DPD: remove unused variable, and convert some constants to MY_EPSILON 2016-12-22 17:05:49 -05:00
stanmoore1 304f65b164 Merge pull request #2 from ibaned/fix-momentum-kokkos 
Fix momentum kokkos from Dan Ibanez
 2016-12-21 12:23:32 -07:00
Dan Ibanez ae8d882b03 need to sync new velocities back to host 2016-12-21 10:57:18 -07:00
Dan Ibanez 7559bc9c5f workaround CUDA View::reference_type 
it is not an lvalue reference in CUDA.
also, the previous code assumed contiguous
entries for one atom; now it should be
robust in the case of LayoutLeft.
 2016-12-21 10:21:55 -07:00
Steve Plimpton 62dea1bb63 21Dec16 patch 2016-12-21 09:53:32 -07:00
sjplimp 800ff43413 Merge pull request #304 from timattox/USER-DPD_whitespace 
USER-DPD: Whitespace cleanup to pair_dpd_fdt_energy.cpp
 2016-12-21 09:51:10 -07:00
Steve Plimpton 9161bd98bf fixed bug with pair hybrid/overaly and manybody potentials finding the right skip neighbor method 2016-12-21 09:50:29 -07:00
Dan Ibanez f3327ca214 allow constructing Few from array on device 2016-12-21 09:21:11 -07:00
Dan Ibanez 54963ba7da allow fix momentum angular with CUDA 2016-12-21 08:55:33 -07:00
Dan Ibanez ea76041803 CUDA-friendly fix_momentum_kokkos angular 2016-12-21 08:54:40 -07:00
Dan Ibanez 7fb4faa439 draft CUDA-callable version of Domain::unmap 2016-12-21 08:53:57 -07:00
Dan Ibanez 41c9357dde allow constructing Few from C array 2016-12-21 08:53:27 -07:00
Dan Ibanez d1a55ad2e0 add kokkos_few.h to .gitignore for /src 2016-12-21 08:07:19 -07:00
Dan Ibanez d9a0f575f6 get fix_momentum_kokkos to compile on White 2016-12-21 08:01:19 -07:00
Dan Ibanez 01e3a31639 put Few in the global namespace... 2016-12-21 08:01:06 -07:00
Dan Ibanez 992becc75f silence warning about partial x2lamda overload 2016-12-21 08:00:42 -07:00
Dan Ibanez 8b5e15e979 add a Makefile for the White testbed 2016-12-20 16:30:50 -07:00
Dan Ibanez b2b33cca16 start working on fix_momentum Kokkos+CUDA 
it doesn't compile anymore,
all in good time...
 2016-12-20 16:30:21 -07:00
Dan Ibanez 2ceee6b9be install kokkos_few, and remove Int 2016-12-20 16:19:17 -07:00
Dan Ibanez 386c12c970 start porting my Few class into this code 2016-12-20 16:09:29 -07:00
Dan Ibanez 590f317550 fix_momentum_kokkos: don't override init() 2016-12-20 11:03:16 -07:00
Tim Mattox c4e02a5d2b USER-DPD: more whitespace fixes 2016-12-20 11:17:11 -05:00
Dan Ibanez c7ac9e79cb preemptive changes for Kokkos+CUDA 
I haven't compiled in that mode yet
(don't know how), but these are some
changes I suspect the compiler
will require.
 2016-12-19 13:17:22 -07:00
Tim Mattox 2ba424e1a3 USER-DPD: Whitespace cleanup to pair_dpd_fdt_energy.cpp 2016-12-19 15:11:52 -05:00
Dan Ibanez ca30c1ec88 got fix_momentum_kokkos to compile 
there are likely still some compile
errors for Kokkos+CUDA...
 2016-12-19 13:08:09 -07:00
Dan Ibanez a1b441a71f draft the parallel_* constructs based on lambdas 
LAMMPS_LAMBDA was added to kokkos_type.h to
facilitate this.

some member variables will likely need local copies
in the fix_momentum code.
 2016-12-19 12:02:12 -07:00
Dan Ibanez f6f2170369 first draft 
copied fix_momentum, work on the Kokkos
View types for the arrays.
the next step is parallel_for and parallel_reduce
transformations.
 2016-12-19 11:28:24 -07:00
Steve Plimpton 81a2db8a0c 17Dec16 patch 2016-12-16 11:36:54 -07:00
Steve Plimpton 0a176841e7 extra python_wrapper change needed for last patch 2016-12-16 11:35:42 -07:00
Steve Plimpton 3027ac9250 patch 16Dec16 2016-12-16 10:30:57 -07:00
sjplimp fc54ab5cea Merge pull request #301 from akohlmey/corrections-and-bugfixes 
Collected corrections and bugfixes
 2016-12-16 10:25:29 -07:00
Steve Plimpton e364b80724 added length keyword to python command 2016-12-16 10:24:25 -07:00
Axel Kohlmeyer 830c9e8661 Merge branch 'USER-DPD_internal_energy' of https://github.com/timattox/lammps_USER-DPD into corrections-and-bugfixes 
This closes #303
 2016-12-16 11:22:25 -05:00
Axel Kohlmeyer 4907b29ad2 Merge branch 'USER-DPD_bugfixes' of https://github.com/timattox/lammps_USER-DPD into corrections-and-bugfixes 
This closes #302
 2016-12-16 11:21:15 -05:00
Tim Mattox eff7238ff2 USER-DPD: fix_eos*: partition all internal energy into the uMech term only 
This makes our results more closely match a vetted serial implementation.
NOTE: This does make the output different from any previous versions.
Patch by Jim Larentzos.  Applied by Tim Mattox.
 2016-12-16 10:25:12 -05:00
Tim Mattox 126fb22e93 USER-DPD: Fix #define typo in pair_multi_lucy.h and pair_multi_lucy_rx.h 2016-12-16 10:08:30 -05:00
Tim Mattox 0a90492c44 USER-DPD: Update the header files to properly document all error statements 
Patch by Jim Larentzos.  Applied by Tim Mattox.
 2016-12-15 17:39:15 -05:00
Tim Mattox fed629c23e USER-DPD: Bugfix for fix_rx and fix_eos_table_rx to handle restart files. 
Patch by Jim Larentzos.  Applied by Tim Mattox.
 2016-12-15 17:10:13 -05:00
Tim Mattox 925481c3f4 USER-DPD: Fix hard-wall force interaction bug, and ensure fraction is >= 0 
pair_exp6_rx.cpp patch by Jim Larentzos.  Applied by Tim Mattox.
 2016-12-15 16:46:25 -05:00
Axel Kohlmeyer da2ad5b6e0 update FixIntel code for new neighbor list code 2016-12-14 15:51:12 -05:00
Axel Kohlmeyer bfcab72268 restore change to make -DLAMMPS_MEMALIGN=64 default when USER-INTEL package is installed (which requires it) 2016-12-14 15:24:55 -05:00
Steve Plimpton f509f133af patch 13Dec16: neighbor refactor, Stan pppm/disp bug fix, M Brown INTEL package updates 2016-12-13 17:14:28 -07:00
sjplimp 624c57e9da Merge pull request #185 from akohlmey/new-neighbor 
New neighbor list code with updates for USER-OMP and USER-DPD
 2016-12-13 16:24:41 -07:00
sjplimp f3b355bcbe Merge pull request #298 from akohlmey/collected-small-fixes 
Collected small fixes
 2016-12-13 16:23:23 -07:00
Steve Plimpton ae5764beac added functionity to lib interface 2016-12-13 16:22:17 -07:00
Axel Kohlmeyer fda43c00fd add deleted file in package to purge list 2016-12-12 13:22:54 -05:00
Stan Moore 13b6196b82 Fixing Kokkos compile error 2016-12-12 10:47:39 -07:00
Stan Moore baf55c90f4 Whitespace change 2016-12-12 09:25:41 -07:00
Stan Moore 770f5d0bf7 Whitespace change 2016-12-12 09:24:37 -07:00
Stan Moore a31b00965a Updating to master 2016-12-12 09:18:20 -07:00
Stan Moore 31be0da590 Merging pull request 2016-12-09 16:17:35 -07:00
Stan Moore 43c459ba56 More changes for Kokkos neighbor 2016-12-09 15:56:55 -07:00
Tim Mattox 5187cb97e5 USER-DPD: Make fix_shardlow request its own SSA-specific neighbor list, 
instead of having pair_dpd_fdt* make the SSA-neighbor list request for it.
Forces an "extra" list to be built, but now skip lists work properly.
Maybe we can detect if skip lists won't be used, and squash the extra list.
 2016-12-09 15:42:27 -06:00
Tim Mattox eff503e56c Prevent neighbor list copies between SSA and non-SSA neighbor list requests. 2016-12-09 15:39:46 -06:00
Axel Kohlmeyer cdcebab3bd make the output of the %CPU/OpenMP threads line consistent with compiling in OpenMP support, not having USER-OMP installed 2016-12-09 14:43:56 -05:00
Stan Moore 435421301b Small tweaks to Kokkos neighbor 2016-12-09 08:37:01 -07:00
Stan Moore 9b48c49f83 Removing used Kokkos file 2016-12-08 09:18:55 -07:00
Stan Moore 8318c67816 Kokkos neighbor refactor 2016-12-07 13:00:27 -07:00
Axel Kohlmeyer 7c61dbf5e2 Merge branch 'new-neighbor' of github.com:akohlmey/lammps into new-neighbor 2016-12-07 13:43:04 -05:00
Axel Kohlmeyer 39a12b15d7 Merge branch 'master' into new-neighbor 
Resolved Conflicts:
	src/Purge.list
	src/neigh_derive.cpp
 2016-12-07 13:40:14 -05:00
Steve Plimpton fb3f597f41 30Nov16 patch 2016-11-30 14:04:41 -07:00
sjplimp d14814ae2e Merge pull request #289 from akohlmey/collected-updates-and-bugfixes 
Collected updates and bugfixes
 2016-11-30 14:02:41 -07:00
Steve Plimpton beb5a30f67 new compute global/atom command, also bug fix for descending dump sorts 2016-11-30 14:01:27 -07:00
Axel Kohlmeyer 789e62388f simplify code 2016-11-29 09:03:53 -05:00
Jakub Krajniak 7d098bff90 update format 
(cherry picked from commit 2597185afb)
 2016-11-29 09:01:36 -05:00
Jakub Krajniak 1d970d3cdf dihedral_nharmonic: added writing coefficient by write_data 
(cherry picked from commit 618f5c6aa5)
 2016-11-29 09:01:36 -05:00
Axel Kohlmeyer 5ff5bc2a6c avoid issues detected by coverity scan 2016-11-28 21:34:35 -05:00
Axel Kohlmeyer 470908fc93 explicitly disallow dynamic groups with compute rdf 2016-11-24 05:46:15 -05:00