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6898 Commits

Author SHA1 Message Date
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
Steve Plimpton 6759630c16 bug fix for dump sort in descending order 2016-11-23 17:08:36 -07:00
Axel Kohlmeyer df46b9aa38 rename compute pressure/grem to compute PRESSURE/GREM 2016-11-22 15:25:59 -05:00
Steve Plimpton 59d100ab57 final prep for 22Nov patch 2016-11-22 09:23:02 -07:00
sjplimp ff0441ac16 Merge pull request #286 from akohlmey/small-fixes-and-updates 
Collected small fixes and updates
 2016-11-22 08:49:46 -07:00
sjplimp 41907d3110 Merge pull request #285 from akohlmey/fix-ipi-update 
update for fix ipi from michele ceriotti
 2016-11-22 08:48:27 -07:00
Steve Plimpton b95f255af4 small changes to temper/grem commands 2016-11-22 08:47:44 -07:00
sjplimp d7b542101a Merge pull request #283 from akohlmey/grem-feature 
gREM generalized replica exchange feature for USER-MISC
 2016-11-22 08:15:35 -07:00
Steve Plimpton 0ffa50f8e8 tweaked author syntax 2016-11-22 08:15:13 -07:00
Axel Kohlmeyer 7893215964 small comment/whitespace tweak 2016-11-21 12:46:43 -05:00
dstelter92 3dff9f2018 removed extra file 2016-11-21 12:05:30 -05:00
dstelter92 dab232c542 modified temper_grem name to fit conventions, re-ran example to match 2016-11-21 12:02:17 -05:00
Michele Ceriotti 87a5a35bad A tiny bugfix for the reset flag, and a brief explanation of the changes 2016-11-20 00:44:23 +01:00
Axel Kohlmeyer e175a18bdb be more thorough in initializing optional data in pair style dpd/fdt/energy 2016-11-18 16:18:47 -05:00
Axel Kohlmeyer a5bde82e37 update .gitignore for recent addition 2016-11-18 15:38:11 -05:00
Axel Kohlmeyer 176cde8ed3 minor cleanups 2016-11-18 15:36:38 -05:00
Axel Kohlmeyer 2862c20815 Merge branch 'master' into grem-feature 2016-11-18 14:51:46 -05:00
Axel Kohlmeyer c78914e7b3 update for fix ipi from michele ceriotti 2016-11-18 09:21:50 -05:00
Axel Kohlmeyer 81f68e06fd Merge branch 'master' into doc-updates 2016-11-17 20:44:07 -05:00
Steve Plimpton 4b51719e67 new 17Nov16 patch and stable 2016-11-17 16:51:35 -07:00
Steve Plimpton 25d7be5f3d compute pressure doc change 2016-11-17 16:11:30 -07:00
sjplimp 74c0e4dd5c Merge pull request #278 from akohlmey/pair-agni 
Implementation of the AGNI manybody potential
 2016-11-17 09:04:31 -07:00
sjplimp 073e8a0524 Merge pull request #276 from akohlmey/doc-updates 
Small bugfixes and updates
 2016-11-17 09:02:27 -07:00
sjplimp 5320bbf585 Merge pull request #275 from andeplane/IP_VORONOI 
Initializing pointers in VORONOI
 2016-11-17 09:01:46 -07:00
sjplimp 4448819824 Merge pull request #274 from andeplane/IP_POEMS 
Initialize pointers in POEMS
 2016-11-17 09:01:37 -07:00
sjplimp 300ac30332 Merge pull request #273 from akohlmey/auto-memalign 
turn on -DLAMMPS_MEMALIGN=64 automatically when USER-INTEL is installed
 2016-11-17 09:01:27 -07:00
sjplimp 2535e44991 Merge pull request #271 from akohlmey/tersoff-modc 
pair style tersoff/mod/c
 2016-11-17 09:00:52 -07:00
sjplimp cdae794383 Merge pull request #242 from andeplane/vashishta_kokkos 
Added KOKKOS vashishta
 2016-11-17 09:00:03 -07:00
Steve Plimpton 8756a1017d Kokkos updates by Stan 2016-11-17 08:58:22 -07:00
dstelter92 5ac2d9532e Re-run example with debug off 2016-11-17 09:43:44 -05:00
dstelter92 19ac9d2959 turned off dev mode by default in temper_grem 2016-11-17 09:31:07 -05:00
dstelter92 07e46b797a added internal tempering in grem with example 2016-11-16 20:27:14 -05:00
Axel Kohlmeyer 82364d10e3 Merge branch 'grem-feature' of https://github.com/dstelter92/lammps into grem-feature 
Resolved merge conflicts and adapted logic to most recent changes in feature branch

Closes #46
 2016-11-16 16:11:53 -05:00
Axel Kohlmeyer 22d93fe8fb add restrict to CCFLAGS for makefiles intended for intel compilers 2016-11-16 14:31:10 -05:00
Axel Kohlmeyer 683f514fac simplify multi-replica run by passing per-replica parameters as variables on the command line 2016-11-16 14:22:20 -05:00
Axel Kohlmeyer f617993944 need to apply fix_modify already in fix grem constructor 2016-11-16 13:52:27 -05:00
Axel Kohlmeyer 705f66aaee remove superfluous code 2016-11-16 13:24:41 -05:00
Axel Kohlmeyer e57ae1ce3f compute scaled kinetic energy tensor without destroying the original data 2016-11-16 12:45:13 -05:00
dstelter92 950442b8b1 added check for nvt vs npt, enabled nvt simulation with fix_grem 2016-11-15 21:53:28 -05:00
Axel Kohlmeyer fdf5d68f9f allow to extract properties in NH integrator only when they are active 2016-11-14 09:27:33 -05:00
Axel Kohlmeyer 0c25f3b1d6 whitespace cleanup 2016-11-13 23:20:09 -05:00
Axel Kohlmeyer 14c7cf4197 retrieve target temperature and pressure from fix npt. add sanity checks. 2016-11-13 23:18:59 -05:00
Axel Kohlmeyer 09544d0698 bugfix for compute pressure/grem: must make a copy of argument strings 2016-11-13 19:19:52 -05:00
Axel Kohlmeyer b5130a3b35 avoid NaN for variance from average output 2016-11-13 18:46:55 -05:00
Axel Kohlmeyer 20daf82463 initial import of adapted gREM code by David Stelter and Edyta Malolepsza 
The following changes were made:
- the modifications to compute pressure were transferred to a derived class compute pressure/grem
- fix scaleforce was renamed to fix grem
- identifying the grem fix was simplified as fix grem passes an additional argument to compute pressure/grem
- dead code was removed in both files
- checking of arguments was tightened
 2016-11-13 18:44:10 -05:00
Axel Kohlmeyer 03b3834fe3 add documentation for pair style agni 2016-11-12 09:07:42 -05:00
Axel Kohlmeyer d0124eac95 optimized data access and using approximate exponential for USER-OMP version 2016-11-12 08:36:27 -05:00
Axel Kohlmeyer 5685131fe2 add USER-OMP version of pair style agni 2016-11-11 19:08:01 -05:00
Axel Kohlmeyer 22fc92f9d8 use special ev_tally() function suitable for this kind of force compute 2016-11-11 18:32:55 -05:00
Axel Kohlmeyer 9cc0c8badd error exit when requested element is not in potential file 2016-11-11 18:10:57 -05:00
Axel Kohlmeyer 9b0987d8c4 first complete implementation of AGNI pair style 2016-11-11 17:32:47 -05:00
Axel Kohlmeyer e453adaf81 implemented parser for 1 element potential files 2016-11-11 15:53:37 -05:00
Axel Kohlmeyer fdcabd7d1d fix addtorque is compatible with dynamic groups 2016-11-11 09:01:18 -05:00
Axel Kohlmeyer c5c8c50e97 initialize 'nper' 2016-11-11 07:47:42 -05:00
Axel Kohlmeyer 801111a7ab dummy framework implementation for AGNI pair style 2016-11-10 15:00:36 -05:00
Axel Kohlmeyer bfc478c320 simpler variant of the segfault workaround, that does not offend Clang c++. 2016-11-10 14:12:02 -05:00
Axel Kohlmeyer 2b75ee761d avoid segmentation fault, when creating a LAMMPS instance from the library interface. arg[] may be NULL. 2016-11-10 13:28:32 -05:00
Anders Hafreager c20ee34c7b Initializing pointers in VORONOI 2016-11-10 09:30:07 +01:00
Anders Hafreager 95a7f7160e Initialize pointers in POEMS 2016-11-10 09:26:52 +01:00
Steve Plimpton 9806da69f3 Stan bug fixes for fix reaxc/bonds/kk 2016-11-09 15:47:50 -07:00
Axel Kohlmeyer fec87c070d simplify compiling USER-INTEL package, by defaulting to -DLAMMPS_MEMALIGN=64 in case it is not set 2016-11-09 16:53:39 -05:00
Axel Kohlmeyer 3e36ec3754 remove unused class member 2016-11-09 16:17:46 -05:00
Axel Kohlmeyer 9ed5c4f0fa Merge branch 'master' into kokkos-vashishta 2016-11-09 15:15:10 -05:00
Axel Kohlmeyer 71ee2ecaa1 integrate pair style tersoff/mod/c contributed by Ganga P Purja Pun (GMU) 
This includes docs, added testing and inclusion of USER-OMP support.
 2016-11-09 14:52:39 -05:00
sjplimp bfea3dce7d Merge pull request #268 from arielzn/born_dsf 
pair styles born/coul/dsf and born/coul/dsf/cs added
 2016-11-09 11:57:09 -07:00
sjplimp eef862ee1c Merge pull request #267 from akohlmey/pager-help 
use pager for help message, if connected to stdout
 2016-11-09 11:53:43 -07:00
sjplimp 0cc2fbf1d6 Merge pull request #266 from andeplane/IP_USER_OMP 
Initializing pointers in USER-OMP
 2016-11-09 11:52:05 -07:00
sjplimp ae00666994 Merge pull request #265 from andeplane/IP_DIFF_DPD 
Initializing pointers in USER-DIFFRACTION and USER-DPD
 2016-11-09 11:51:53 -07:00
sjplimp 51b3b5fb35 Merge pull request #264 from andeplane/IP_SNAP_SRD 
Initialize pointers in SNAP and SRD
 2016-11-09 11:51:44 -07:00
sjplimp 176f2c3aa1 Merge pull request #263 from andeplane/IP_RIGID_SHOCK 
Initialize pointers in RIGID and SHOCK
 2016-11-09 11:51:36 -07:00
sjplimp 3f71bfb185 Merge pull request #262 from andeplane/IP_PERI_QEQ_REPLICA 
Initializing pointers in PERI, QEQ and REPLICA
 2016-11-09 11:51:25 -07:00
sjplimp cf3ab51679 Merge pull request #261 from andeplane/IP_MISC_MOLECULE 
Initialized pointers in MISC and MOLECULE
 2016-11-09 11:51:09 -07:00
sjplimp 59922f894b Merge pull request #260 from andeplane/IP_MANYBODY_MC 
Initialize pointers in MANYBODY and MC
 2016-11-09 11:51:01 -07:00
sjplimp 5e2b9d8bf3 Merge pull request #259 from andeplane/IP_KSPACE 
Initialize pointers in KSPACE
 2016-11-09 11:50:50 -07:00
sjplimp 2d132cad6b Merge pull request #258 from andeplane/IP_GRANULAR 
Initialize pointers in GRANULAR
 2016-11-09 11:50:41 -07:00
sjplimp ef6801f8bf Merge pull request #257 from andeplane/IP_CORESHELL 
Initialize pointers in CORESHELL
 2016-11-09 11:50:31 -07:00
sjplimp c81a723642 Merge pull request #256 from andeplane/IP_BODY 
Initialized pointers in BODY
 2016-11-09 11:50:23 -07:00
sjplimp f9eb2a99ce Merge pull request #255 from andeplane/IP_ASPHERE 
Initialize pointers in ASPHERE
 2016-11-09 11:50:11 -07:00
sjplimp 16a02ef27d Merge pull request #254 from andeplane/IP_root 
Initialized pointers in src folder
 2016-11-09 11:47:21 -07:00
Steve Plimpton 2c801320c2 fixed links in Section_intro.txt 2016-11-09 11:46:10 -07:00
Anders Hafreager d20b32092e Building correct shortlists and removed rsq test in force loops 2016-11-08 18:57:27 +01:00
arielzn cdb5d47e9f add FLERR argument to force->bounds() in born/coul/dsf 2016-11-08 18:24:54 +01:00
Steve Plimpton a23b287a7a sync with SVN for creation of stable release 2016-11-08 09:05:50 -07:00
Steve Plimpton 31204aab6a sync with SVN 2016-11-08 08:57:51 -07:00
arielzn 667f4dfe28 pair style born/coul/dsf added with its coreshell version 2016-11-08 11:32:38 +01:00
Axel Kohlmeyer 21694ca3a8 improve help and it through a pager, when screen == stdout 2016-11-07 17:10:12 -05:00
Axel Kohlmeyer 9b910d5511 make name of the actual executable (i.e. arg[0]) accessible 2016-11-07 17:07:40 -05:00
Anders Hafreager 054ab6bff3 Initializing pointers in USER-OMP 2016-11-07 21:07:10 +01:00
Anders Hafreager 616420cda8 Initializing pointers in USER-DIFFRACTION and USER-DPD 2016-11-07 20:51:36 +01:00
Anders Hafreager fb3ac9afba Initialize pointers in SNAP and SRD 2016-11-07 20:30:38 +01:00
Anders Hafreager 7cd7cda2d4 Initialize pointers in RIGID and SHOCK 2016-11-07 20:22:04 +01:00
Anders Hafreager db0524278a Initializing pointers in PERI, QEQ and REPLICA 2016-11-07 19:58:27 +01:00
Anders Hafreager 1ff75eaba2 Initialized pointers in MISC and MOLECULE 2016-11-07 17:15:48 +01:00
Anders Hafreager 30dede867a Initialize pointers in MANYBODY and MC 2016-11-07 17:02:32 +01:00
Anders Hafreager a5c6104d64 Initialize pointers in KSPACE 2016-11-07 16:54:59 +01:00
Anders Hafreager c5869bdee2 Initialize pointers in GRANULAR 2016-11-07 16:33:50 +01:00
Anders Hafreager e7a2c6b5d1 Initialize pointers in CORESHELL 2016-11-07 16:26:16 +01:00
Anders Hafreager 06959a9c59 Initialized pointers in BODY 2016-11-07 16:21:08 +01:00
Anders Hafreager cd65d44d95 Initialize pointers in ASPHERE 2016-11-07 16:15:39 +01:00
Anders Hafreager 45f2e86dd6 NULLed ptrs in files 2016-11-07 16:07:37 +01:00
Anders Hafreager f8226e8ae5 NULL ptrs in dump_custom and dump_image 2016-11-07 15:56:47 +01:00
Anders Hafreager b221b15d24 NULLing ptrs in comm_brick and dump*.cpp 2016-11-07 15:50:18 +01:00
sjplimp f0131393e0 Merge pull request #248 from akohlmey/collected-small-fixes 
collected small bugfixes and updates
 2016-11-04 10:58:42 -06:00
sjplimp 32e0a58343 Merge pull request #247 from akohlmey/bounds-error-with-code-line 
Propagate error error locations for a few more utility functions
 2016-11-04 10:58:14 -06:00
sjplimp 60908eeab4 Merge pull request #246 from akohlmey/manybody-short-neighbor-list 
Manybody short neighbor list
 2016-11-04 10:57:43 -06:00
sjplimp 8214555b29 Merge pull request #244 from ketankhare/patch-2 
Enable write_data for dihedral style fourier
 2016-11-04 10:57:20 -06:00
Steve Plimpton f48b71f46b added examples/threebody, fix reaxc/speceies/kk 2016-11-04 10:56:04 -06:00
Axel Kohlmeyer 7d23a0737e add thorough checking for valid arguments to -partition or -p 2016-11-04 00:42:23 -04:00
Axel Kohlmeyer 02510ec321 add temporary force accumulation to local variables for vashishta styles 2016-11-02 22:32:30 -04:00
Axel Kohlmeyer 33140e5004 accumulate forces in temporary local variables for tersoff 2016-11-02 22:16:53 -04:00
Axel Kohlmeyer 639fb6f444 use local variables for more efficient force accumulation 2016-11-02 17:20:56 -04:00
Axel Kohlmeyer b156771721 build short neighbor list for sw on based on ij parameters only 2016-11-02 17:09:32 -04:00
Axel Kohlmeyer 5d787f7f16 avoid tiny memory leak, when the restart command is specified multiple times 2016-11-01 21:39:12 -04:00
Axel Kohlmeyer c8f4b55588 avoid uninitialized data for using ewald/disp with lj only 2016-11-01 16:48:30 -04:00
Axel Kohlmeyer e13e4031cf avoid memory leak in pppm/disp/omp 2016-11-01 16:48:00 -04:00
Axel Kohlmeyer 782a328080 avoid memory leaks when using kspace solvers for lennard-jones 2016-11-01 14:55:13 -04:00
Axel Kohlmeyer e81ae21dbd do not access uninitialized data for ewald/disp and pppm/disp 2016-11-01 14:54:16 -04:00
Anders Hafreager f333d659c2 Using short neighborlists in neigh full 2016-10-29 22:54:43 +02:00
Anders Hafreager 51e2313fac Using short neighbor lists 2016-10-29 22:35:29 +02:00
Anders Hafreager e37d2b5c94 Calculating short neighbor lists 2016-10-29 22:20:37 +02:00
Axel Kohlmeyer c4b86a25a7 Merge branch 'master' into manybody-short-neighbor-list 2016-10-28 11:12:21 -04:00
Axel Kohlmeyer 218e121b41 Merge branch 'master' into bounds-error-with-code-line 2016-10-28 11:11:28 -04:00
Axel Kohlmeyer 4216be49f3 Merge branch 'master' into collected-small-fixes 2016-10-28 10:46:33 -04:00
Axel Kohlmeyer 3870780894 Merge branch 'master' into kokkos-vashishta 2016-10-28 10:43:05 -04:00
Steve Plimpton d9891abdf4 new library functions 2016-10-27 09:34:04 -06:00
Axel Kohlmeyer f9a9e27f5a add error location propagation to atom->set_mass() and atom->check_mass() 2016-10-26 16:01:40 -04:00
Axel Kohlmeyer 35753b8f08 add error location propagation to force->bounds() and force->boundsbig() 2016-10-26 15:53:02 -04:00
Axel Kohlmeyer f028a9a967 region cylinder is compatible with open_faces[2], so do not disallow it. 2016-10-26 15:04:18 -04:00
Axel Kohlmeyer ef9f7c818e fix off-by-one bug in buffer re-allocator 2016-10-26 10:14:08 -04:00
Axel Kohlmeyer 8e61bed2d8 add USER-OMP variant of manybody short neighbor list 2016-10-26 09:51:52 -04:00
Axel Kohlmeyer 3267b34590 simplify short neighbor list implementation. remove unneeded class member 2016-10-26 09:29:27 -04:00
Axel Kohlmeyer 0a417b4016 add short neighbor list support to pair style tersoff 2016-10-26 07:06:38 -04:00
Axel Kohlmeyer 399c0af150 consistent short neighbor list for vashishta and vashishta/table 2016-10-25 23:46:25 -04:00
Axel Kohlmeyer e8b3f79690 fully tested multi-element compatible short neighbor list for Stillinger-Weber 2016-10-25 23:18:14 -04:00
stamoor 21619f6a2f Recommitting reverted change 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15794 f3b2605a-c512-4ea7-a41b-209d697bcdaa
(cherry picked from commit c0b98f5299)
 2016-10-25 15:25:39 -04:00
Anders Hafreager 039bda9b61 Added updated vashishta for KOKKOS support 
(cherry picked from commit 96089a42547f625e70aa2ac3933d248d2731b731)
 2016-10-25 15:07:10 -04:00
Anders Hafreager 6929603eef Added KOKKOS vashishta 
(cherry picked from commit 5edc474bf0be574ddba96d00bb63894edf400ddb)
 2016-10-25 15:07:10 -04:00
ketankhare 7f3f5e8c38 Clean whitespace 2016-10-25 14:46:44 -04:00
ketankhare f350500e69 Enable write_data 2016-10-25 14:43:12 -04:00
ketankhare d7c77a419d Enable write_data for dihedral_fourier 2016-10-25 14:36:18 -04:00
sjplimp efaa8feab5 Merge pull request #239 from akohlmey/static-analysis-fixes 
Static analysis fixes
 2016-10-25 10:32:55 -06:00
Axel Kohlmeyer ba6d1528bb Merge branch 'colvars-2016-10-24' of https://github.com/giacomofiorin/lammps into colvars-update 2016-10-24 17:34:28 -04:00
Giacomo Fiorin 182141b850 Make SMP parallelism for Colvars optional 2016-10-24 17:13:34 -04:00
Axel Kohlmeyer 512c413b7e whitespace cleanup 2016-10-24 17:13:21 -04:00
Axel Kohlmeyer 7b89e47a38 apply corrections to issues reported by static code analysis 2016-10-24 17:12:28 -04:00
Axel Kohlmeyer db36c8bcc3 stop with error, if molecule command requires special bond auto-generation before box is defined 2016-10-21 14:51:09 -04:00
Axel Kohlmeyer 991034b632 have bond style table exit when bond length is outside table range 2016-10-21 14:01:06 -04:00
Axel Kohlmeyer a2e34aab0a make certain, that atom->maxspecial is incremented with extra special space 2016-10-21 11:55:36 -04:00
Steve Plimpton 9954d5d346 forgot pair table change 2016-10-19 10:47:07 -06:00
Steve Plimpton 3d254780de Merge branch 'master' of github.com:lammps/lammps 2016-10-19 08:58:22 -06:00
sjplimp b0cf1ded38 Merge pull request #229 from akohlmey/small-corrections 
collected various small corrections and updates
 2016-10-19 08:57:54 -06:00
sjplimp 0891ed83a5 Merge pull request #228 from akohlmey/correct-prd-for-bigbig 
make PRD code compatible with -DLAMMPS_BIGBIG
 2016-10-19 08:56:19 -06:00
Axel Kohlmeyer ffb8eb36da Revert "recognize any word starting with FP as FPRIME style table" 
This reverts commit 86f5b51133.
 2016-10-19 10:44:38 -04:00
Axel Kohlmeyer 1a10857244 make PRD code compatible with -DLAMMPS_BIGBIG 2016-10-19 10:43:25 -04:00
Axel Kohlmeyer 2634468676 dead code removal 2016-10-19 10:42:02 -04:00
Steve Plimpton 58141e0559 text edit 2016-10-19 08:41:44 -06:00
sjplimp 393337e7cf Merge pull request #226 from akohlmey/pair-gauss-mixing 
add mixing support for pair styles gauss and gauss/cut
 2016-10-19 08:37:32 -06:00
sjplimp e0ed218cc4 Merge pull request #224 from akohlmey/get-vars 
provide an accessor for names of LAMMPS variables
 2016-10-19 08:36:52 -06:00
Axel Kohlmeyer 86f5b51133 recognize any word starting with FP as FPRIME style table 2016-10-19 09:05:25 -04:00
Axel Kohlmeyer ccca642b3a fix typo 2016-10-19 08:08:52 -04:00
Axel Kohlmeyer 7b7cb297e6 add mixing for pair styles gauss and gauss/cut contributed by andrew jewett. also add support for write_data. 2016-10-18 22:26:47 -04:00
Axel Kohlmeyer 5a6dea7a22 Merge branch 'master' into user-nc-dump 2016-10-18 15:36:18 -04:00
Steve Plimpton 2106dce2b3 new fix halt command, other sundry small bug fixes 2016-10-18 13:11:40 -06:00
Axel Kohlmeyer 6e54443d8c make plain nc dump style a compile time option as well 
according to the package author, lars pastewka, some machines
may have only parallel netcdf and not the serial netcdf installed.
hence both netcdf dump styles neet to be optional depending on
the compile time setting in lib/netcdf/Makefile.lammps
The makefile has been set up to auto-detect the necessary flags
for most regular and correct installations.
 2016-10-18 15:11:22 -04:00
Axel Kohlmeyer ae77664bdd forgot to include USER-NC-DUMP in PACKUSER variable 2016-10-18 14:45:25 -04:00
Axel Kohlmeyer 1f7693faf2 fix typo 2016-10-18 14:06:43 -04:00
Axel Kohlmeyer 2c5ea9fc61 reapply changes to the timer class that got lost somehow 2016-10-18 14:05:08 -04:00
Axel Kohlmeyer 3e88fb5355 Merge branch 'master' into collected-bugfixes 2016-10-18 13:54:15 -04:00
Steve Plimpton 003581c6a8 final changes to fix halt 2016-10-18 11:16:28 -06:00
Axel Kohlmeyer 1f1c87235a add support for "error continue" option, which resets the timer timeout setting after a soft exit 2016-10-18 12:21:27 -04:00
Axel Kohlmeyer 394c3bb504 add Timer::reset_timeout() API, that allows restoring the previous timeout setting after a forced timeout 2016-10-18 12:20:49 -04:00
Steve Plimpton 954d536826 added bondmax method to fix halt 2016-10-18 09:27:01 -06:00
Axel Kohlmeyer c5513c4f75 provide an accessor for names of LAMMPS variables 2016-10-17 19:56:18 -04:00
Axel Kohlmeyer e7825ba21a import fix halt prototype code with corrections for soft exit 2016-10-15 07:30:07 -04:00
Axel Kohlmeyer e77e1f6b8e replace complex solution to implement a soft exit with simpler one 2016-10-14 19:40:51 -04:00
Axel Kohlmeyer 909ec2c096 remove unused class members 2016-10-14 12:04:32 -04:00
Axel Kohlmeyer f67975fd8a apply proper initialization and remove redundant variable declaration 2016-10-14 07:37:06 -04:00
Axel Kohlmeyer deceb9d5c6 remove assignment without effect 2016-10-14 07:31:52 -04:00
Axel Kohlmeyer c9c66ca0bd replace unsafe code 2016-10-14 07:28:25 -04:00
Axel Kohlmeyer d07703efff re-apply bugfix from two years ago 2016-10-14 07:27:40 -04:00
Axel Kohlmeyer 411ecca8df plug memory leak 2016-10-14 07:27:14 -04:00
sjplimp 40f2310a2a Merge pull request #218 from timattox/USER-DPD_fix_rx_init_bugfix 
USER-DPD fix_rx initialization bugfix
 2016-10-13 16:56:19 -06:00
Steve Plimpton 2c8a7a318a bug fix for fix GCMC w/ fix shake, enhance of fix wall/gran/region with restarting 2016-10-13 16:55:53 -06:00
Tim Mattox fcb5271026 USER-DPD: Initialize the dpdThetaLocal array consistently in fix_rx 2016-10-12 15:56:45 -04:00
Tim Mattox 4958e114ba USER-DPD bugfix: Properly initialize the local temperature averaging array. 2016-10-12 15:46:46 -04:00
Steve Plimpton 63e71cd45b patch to add DPD-VV 2016-10-12 07:35:47 -06:00
sjplimp 4a5d9eaae2 Merge pull request #217 from akohlmey/small-fixes 
Collected small changes and bugfixes
 2016-10-12 07:32:08 -06:00
sjplimp 4e3a55047f Merge pull request #215 from timattox/USER-DPD_bugfix_for_dtsqrt 
USER-DPD Bugfix: reset_dt() is not called when I thought it should be called.
 2016-10-12 07:30:10 -06:00
Axel Kohlmeyer f8a26dd158 update Timer::force_timeout() to trigger at next loop iteration 2016-10-12 07:26:03 -04:00
Axel Kohlmeyer 2e8edbd2b9 USER-SMD was missing from PACKLIB variable 2016-10-12 06:53:37 -04:00
Axel Kohlmeyer da66c1e649 update #include directives to match current LAMMPS coding conventions 2016-10-12 00:07:52 -04:00
Axel Kohlmeyer c24bf512f3 update #include statements for system includes 2016-10-12 00:00:53 -04:00
Axel Kohlmeyer 6b4ab0a390 update .gitignore 2016-10-12 00:00:21 -04:00
Axel Kohlmeyer adc98e07df whitespace cleanup in USER-DPD 2016-10-11 23:58:36 -04:00
Axel Kohlmeyer 69cb831705 import dump nc and dump nc/mpiio from lammps-netcdf as USER-NC-DUMP package by lars pastewka 2016-10-11 23:44:34 -04:00
Axel Kohlmeyer ecb03dd2df import lammps-netcdf code as USER-NC-DUMP package 2016-10-11 23:03:18 -04:00
Tim Mattox 2f07a627a2 Forgot to remove my call to reset_dt() 2016-10-11 16:30:41 -04:00
Tim Mattox 559637f4bc USER-DPD Bugfix: reset_dt() is not called when I thought it should be called. 
Move the calculation of dtsqrt inside FixShardlow::initial_integrate()
 2016-10-11 16:11:29 -04:00
sjplimp fbf7df14b5 Merge pull request #212 from timattox/USER-DPD_fix_eos_atom_style_checks 
USER-DPD: Add atom_style compatibility checks in fix_eos_*.cpp files.
 2016-10-11 13:40:00 -06:00
sjplimp 6f1162927a Merge pull request #207 from timattox/USER-DPD_new_VV_for_DPD 
USER-DPD: add support for using VV with DPD
 2016-10-11 13:39:25 -06:00
sjplimp 803dc57bfa Merge pull request #214 from akohlmey/make-no-lib-no-mpiio 
make no-lib should also remove MPIIO and USER-LB packages
 2016-10-11 12:42:53 -06:00