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6898 Commits

Author SHA1 Message Date
sjplimp f5a85d68ad Merge pull request #429 from akohlmey/updates-for-stable 
Collected updates for stable release
 2017-03-24 10:01:23 -06:00
sjplimp 277b93cb89 Merge pull request #417 from tonnamb/add-pair-zhou 
add new pair potential for metal-organic interactions - pair style momb
 2017-03-24 09:41:30 -06:00
Axel Kohlmeyer 8820315ff9 Merge branch 'master' into updates-for-stable 2017-03-23 17:57:02 -04:00
Steve Plimpton 44841f6891 fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof 2017-03-23 15:31:27 -06:00
Axel Kohlmeyer 47cade2bcf re-arranged functions to make it easier to compare with non-threaded. port bugfixes to airebo to USER-OMP 2017-03-23 15:19:02 -04:00
Axel Kohlmeyer a72efbea36 whitespace cleanup 2017-03-23 15:18:23 -04:00
Axel Kohlmeyer 5c9892c083 apply airebo/m bugfix also to USER-OMP version 2017-03-23 14:14:49 -04:00
Axel Kohlmeyer 9ecc5c8cf7 Merge branch 'fix-airebo-morse' of https://github.com/v0i0/lammps into pull-431 2017-03-23 14:12:37 -04:00
Markus Hoehnerbach 47cebb0d23 And getting it right... 2017-03-23 17:43:27 +01:00
Markus Hoehnerbach f127e428cc Fix airebo/morse 
Introduced in b3d2fb91, PCCf_2_0 does not get initialized in ::settings
in PairAIREBOMorse. Future proof by calling super-class.
 2017-03-23 17:37:49 +01:00
Axel Kohlmeyer 568b67eee9 include citation for reference paper into pair style momb 2017-03-23 12:00:53 -04:00
Axel Kohlmeyer b88a749680 rename a couple more references to pair style zhou into momb 2017-03-23 11:38:33 -04:00
Tonnam Balankura 343c9eda82 change zhou to momb in src/USER-MISC/README 2017-03-23 10:24:13 -04:00
Tonnam Balankura df8dbec676 rename pair_zhou to pair_momb in src and change class name from PairZhou to PairMomb 2017-03-23 10:22:49 -04:00
Tonnam Balankura daae76c465 Add names Tonnam and Ya to README 2017-03-22 15:59:00 -04:00
Tonnam Balankura 1ea9a14121 Add Tonnam and Ya names 2017-03-22 15:55:34 -04:00
Axel Kohlmeyer dc1d93a491 some more whitespace cleanup 2017-03-22 15:08:09 -04:00
Axel Kohlmeyer cb9059652d a few more small changes to integrate pair style zhou properly 2017-03-22 14:39:46 -04:00
Axel Kohlmeyer 43f27250b5 Merge branch 'add-pair-zhou' of https://github.com/tonnamb/lammps into pull-417 2017-03-22 14:05:16 -04:00
Oliver Henrich af0b5b0e84 Removed dead code 2017-03-22 16:23:29 +00:00
Oliver Henrich 7435084375 Verified oxDNA with modified nucleotide layout 2017-03-22 15:59:10 +00:00
Steve Plimpton dcede304df changes for next patch, 2d disc options for spheres, fix external upgrade, bug fixes for fix ave/chunk for density calcs, Aidan doc page citation deconvolution 2017-03-21 08:56:37 -06:00
Axel Kohlmeyer 554531a302 update permissions 2017-03-20 13:51:36 -04:00
dstelter92 5b842f0010 Teff and exchange bugfix, as per Greg Dignon to match python examples 2017-03-20 09:15:48 -04:00
Tonnam Balankura b6ecfb91c4 deleted pair_zhou in main/src (moved to USER-MISC) 2017-03-18 21:22:02 -04:00
Tonnam Balankura 2ab77caa8b adapt to LAMMPS coding style 2017-03-18 21:01:40 -04:00
Tonnam Balankura da81531906 move pair_zhou to USER-MISC and update USER-MISC/README 2017-03-18 20:54:12 -04:00
Tonnam Balankura 5be32f5d8d remove pair_zhou from Makefile.list 2017-03-18 20:48:49 -04:00
Steve Plimpton 4a90bca7a3 patch 17Mar17 2017-03-17 11:29:23 -06:00
sjplimp 9f35b764f8 Merge pull request #424 from timattox/dpd_restart_fix 
Remove unneeded restart_peratom flags in USER-DPD package
 2017-03-17 11:19:04 -06:00
sjplimp 7ca5dce2f5 Merge pull request #423 from timattox/master_bugfix_irregular 
bugfix for irregular::create_atom and create_data
 2017-03-17 11:18:52 -06:00
sjplimp fcc3b3bd36 Merge pull request #421 from akohlmey/memory-output 
improve memory usage reporting in info and output class
 2017-03-17 11:18:08 -06:00
sjplimp a936b7b2ab Merge pull request #419 from rbberger/python_fixes 
Library interface fixes, Python example fixes and better Python 3 compatibility
 2017-03-17 11:16:58 -06:00
Stan Moore d31c591b60 Remove unneeded restart_peratom flags 2017-03-17 09:40:39 -06:00
Axel Kohlmeyer ae5ebf6001 add support for MPI_Request_free() to MPI STUBS library 2017-03-17 11:40:09 -04:00
Axel Kohlmeyer 7fb741d53d Revert "In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block()" 
This reverts commit 8e75616c14.
 2017-03-17 11:35:59 -04:00
Tim Mattox 8e75616c14 In irregular.cpp use simpler and slightly faster MPI_Reduce_scatter_block() 2017-03-17 03:02:42 -04:00
Tim Mattox 411c069ba6 BUGFIX: Prevent possible deadlock in Irregular::create_atom and create_data 2017-03-17 03:02:19 -04:00
Axel Kohlmeyer ac82d041cc ignore package pair style 2017-03-16 23:12:49 -04:00
Axel Kohlmeyer 070ce33a13 improve memory usage reporting in info and output class 2017-03-16 18:35:04 -04:00
Axel Kohlmeyer f604f86cfc add fix filter/corotate to some administrative files 2017-03-16 15:08:17 -04:00
Axel Kohlmeyer 1995f434f3 fix some more code formatting issues, add newline at EOF 2017-03-16 14:24:28 -04:00
lukin17 2f5e711acd Merge remote-tracking branch 'upstream/master' into filter_corotate 2017-03-16 10:00:12 +01:00
lukin17 bdb7669e27 Fixed coding style. 2017-03-16 09:44:07 +01:00
Richard Berger a210867025 Fixes lammps_create_atoms library function and its Python interface variant 
The interface of that function has changed and includes two additional
parameters, which haven't been added to the Python interface either.
This showed up by trying to run the simple.py example.
 2017-03-15 22:13:06 -04:00
sjplimp 3a2da51a82 Merge pull request #413 from ohenrich/user-cgdna 
User cgdna
 2017-03-15 13:12:43 -06:00
Tonnam Balankura ec1778b586 add pair_zhou 2017-03-15 11:10:04 -04:00
lukin17 c3ce3747e0 Added fix filter/corotate. 2017-03-15 11:34:01 +01:00
Stan Moore 580f6b567b Add neigh/qeq option to Kokkos 2017-03-14 10:44:31 -06:00
Oliver Henrich 7a75cd111c Minor updates in documentation and setup tool, merge before upgrade to oxDNA2 2017-03-14 11:39:09 +00:00
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