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11293 Commits

Author SHA1 Message Date
Julien Guénolé 426ca97aa6 correct bug introduced in previous commit 2020-01-29 17:53:10 +01:00
Julien Guénolé 1e7f09bded removing deprecated functions in log comment 2020-01-29 17:50:56 +01:00
Axel Kohlmeyer c855bbb6bf
Merge branch 'master' into adaptglok 2020-01-29 11:42:25 -05:00
Giacomo Fiorin 9427fc50a5 Update Colvars library to version 2020-01-27 
One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
 2020-01-28 14:15:05 -05:00
Julien Guénolé 197ba62cd9 Change fire to fire/old and fire2 to fire. Implement normstyle in fire. Update author affiliation. 2020-01-28 14:51:23 +01:00
Axel Kohlmeyer 795f2fd894
properly support threaded FFTs with MKL and document it. remove commented out FFTW2 code 2020-01-27 11:00:57 -05:00
Axel Kohlmeyer 4134d7fddd
Merge pull request #1854 from akohlmey/next_patch_release 
Update version string for the next patch release
 2020-01-24 20:58:03 -05:00
Stan Moore 669980388a Merge branch 'fft' of ssh://github.com/stanmoore1/lammps into fft 2020-01-24 14:33:31 -07:00
Stan Moore 76aaf16c66 Add check for FFT_FFTW_THREADS and turn off MKL threads for now 2020-01-24 14:30:11 -07:00
Stan Moore e9d4823d71 Add cuFFT to Makefile.lassen_kokkos and generalize MPI path 2020-01-24 13:56:00 -07:00
Oliver Henrich 899a654161 Merge branch 'master' into user-cgdna 2020-01-24 14:21:55 +00:00
Oliver Henrich 23febc7101 Increased tolerance for fatal error in FENE bond argument 2020-01-24 14:19:18 +00:00
Axel Kohlmeyer cb5138a335
update version string for the next patch release 2020-01-23 12:00:33 -05:00
Axel Kohlmeyer df23460e18
Merge branch 'master' into fft 
# Conflicts:
#	src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 2020-01-23 00:22:38 -05:00
Axel Kohlmeyer 30444b344b
Merge pull request #1853 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for the next patch release
 2020-01-22 17:25:03 -05:00
Axel Kohlmeyer 8096a78340
Merge pull request #1852 from vklip/bugfix-gjf 
Add unit conversion in setup() in fix_langevin.cpp
 2020-01-22 17:22:01 -05:00
Axel Kohlmeyer 949d7608ba
Merge pull request #1811 from brycelelbach/bug/missing_execution_space_qualifiers 
Fix mismatches in CUDA execution space qualifiers between declarations and definitions.
 2020-01-22 17:10:11 -05:00
Axel Kohlmeyer 5488efbc03
fix typo, update maintainer. 2020-01-22 17:00:10 -05:00
Axel Kohlmeyer 70731468df
include "pppm.h" last so that necessary KOKKOS config define is available 2020-01-22 16:32:32 -05:00
Axel Kohlmeyer 9d06430894
Merge pull request #603 from jrgissing/Ncreate_atoms 
add exactly N particles to available lattice points
 2020-01-22 15:36:54 -05:00
Axel Kohlmeyer 61ddf9bcd8
undo accidental edit of KOKKOS cuda mpi makefile 2020-01-22 15:32:00 -05:00
Axel Kohlmeyer 70b9a060dc
add missing #endif 2020-01-22 15:26:34 -05:00
Axel Kohlmeyer 9a27aa4e9e
Merge branch 'master' into fft 
# Conflicts:
#	src/MAKE/OPTIONS/Makefile.kokkos_cuda_mpi
 2020-01-22 15:21:08 -05:00
Axel Kohlmeyer dfda8b5ce6
fix up LMP_FFT_LIB for reporting FFT lib in use for KOKKOS with CUDA logic 2020-01-22 15:18:59 -05:00
Axel Kohlmeyer 40e0e78abd
import template atom ID check from PR #1822 2020-01-22 15:02:55 -05:00
Axel Kohlmeyer bb024bc077
add call to KSpace::two_charge() that was overlooked 2020-01-22 14:46:57 -05:00
Axel Kohlmeyer 48cae2703b
move memory allocation for atom style variable data where it belongs and cannot be skipped 
this fixes the bug reported on lammps-users on 2020-01-22 by Olivier Politano
 2020-01-22 14:34:12 -05:00
Axel Kohlmeyer cc81dc2046
remove redundant initializers 2020-01-22 14:32:34 -05:00
Axel Kohlmeyer 37e8195b01
fix whitespace issue 2020-01-22 12:44:24 -05:00
Axel Kohlmeyer a87c7a4a53
avoid segfault 2020-01-22 12:41:59 -05:00
Axel Kohlmeyer 0623859f36
fix small bug in pair style extep 2020-01-22 11:25:13 -05:00
Viktor Klippenstein 0ae40c5967 Add unit conversion in setup() 2020-01-22 17:13:10 +01:00
jrgissing d897949ff8 bond/react: check for valid IDs in map file 2020-01-21 23:21:41 -07:00
Steve Plimpton ac143dbdb7 capitalize comment 2020-01-21 17:57:12 -07:00
Steve Plimpton 11f687c1fb make comment string consistent 2020-01-21 17:56:00 -07:00
Steve Plimpton b29ffabe56 move two_charge_force calc to occur at init, not constructor 2020-01-21 14:24:55 -07:00
Axel Kohlmeyer a6f59a8607
Merge remote-tracking branch 'github/master' into Ncreate_atoms 
# Conflicts:
#	src/create_atoms.cpp
 2020-01-21 15:52:01 -05:00
Axel Kohlmeyer 646dc83394
remove trailing whitespace 2020-01-21 15:46:28 -05:00
Steve Plimpton d83cf8e4b0 add Jake's name as contributor 2020-01-21 13:36:36 -07:00
Steve Plimpton 90ff2eb6c9 modified versions of creating atoms on subset of lattice, ditto for set type/fraction 2020-01-21 13:31:47 -07:00
Steve Plimpton 4ea679dd54 Merge branch 'master' into nparticles 2020-01-21 13:26:03 -07:00
Axel Kohlmeyer 12de17621f
Merge branch 'master' into collected-small-changes 
# Conflicts:
#	doc/src/Commands_fix.rst
 2020-01-20 16:59:42 -05:00
Axel Kohlmeyer 795a872bf3
Merge pull request #1847 from pdebuyl/fix-active 
Add fix propel/self
 2020-01-20 16:57:04 -05:00
Axel Kohlmeyer f03cfba029
Merge pull request #1820 from ornladios/adios_read_dump 
Support read_dump with dump style 'adios'
 2020-01-20 16:27:09 -05:00
Axel Kohlmeyer 946bd8f3c0
print warning about adjusting the communication cutoff only during integrator or minimizer setup phase 2020-01-20 16:23:26 -05:00
Pierre de Buyl 7766b29c97 replace strncmp by strcmp 2020-01-20 21:54:29 +01:00
Podhorszki Norbert 44a814ec1d Added 'timeout <value>' option to the adios reader, so that a rerun can concurrently run with the first simulation 2020-01-20 15:52:21 -05:00
Pierre de Buyl 3ccab876f7 fix string length for strncmp 2020-01-20 18:16:20 +01:00
Pierre de Buyl 8ed271f16f change mode of propel/self to quat instead of quaternion 2020-01-20 17:41:20 +01:00
Podhorszki Norbert 18c16b4b39 Print lammps style error and abort when adios2_config.xml is not found. Avoid ugly C++ exception stack. 2020-01-20 10:11:57 -05:00
Axel Kohlmeyer 125a82f572 change isReaderParallel flag to parallel and generally adapt more to LAMMPS programming style 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer 76818a47c0 add missing include statement 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer fed1e800a9 revert reformatting of unrelated file 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer 9959997376 change attribution 2020-01-20 09:20:42 -05:00
Podhorszki Norbert 0da85cb2fc update README for USER-ADIOS 2020-01-20 09:20:42 -05:00
Podhorszki N 580909fd47 Implement read_dump with format 'adios'. It modifies read_dump.cpp to support reading from one dataset by all processes. 2020-01-20 09:20:42 -05:00
Axel Kohlmeyer 0bed348073
fix typo 2020-01-20 07:17:39 -05:00
Axel Kohlmeyer 019e269ed9
silence compiler warning 2020-01-20 07:12:22 -05:00
Axel Kohlmeyer 3ff49dfd59
avoid segfault when using per-particle masses 2020-01-20 07:12:12 -05:00
Axel Kohlmeyer c19085dc08
silence compiler warning 2020-01-20 07:06:49 -05:00
Axel Kohlmeyer 926096dc66
silence compiler warning 2020-01-20 07:06:00 -05:00
Vsevak d1f3f659ac Fix GPU package install script to resolve file dependency 
'pair_lj_cut_tip4p_long_gpu' depends on 'pair_lj_cut_tip4p_long' from KSPACE package
 2020-01-20 00:03:04 +03:00
Axel Kohlmeyer 074e18d9cb
fix one more whitespace issue 2020-01-19 13:34:21 -05:00
Axel Kohlmeyer 0471d211a2
remove dead code and silence compiler warnings 2020-01-19 13:33:16 -05:00
Axel Kohlmeyer 5e740c9cc5
documentation and examples cleanup for fix propel/self 
- rename example folder
- remove .txt format docs
- remove obsolete fix active sources
- update readme in src/USER-MISC
- replace non-ASCII characters and fix spelling issues
 2020-01-19 13:29:52 -05:00
Axel Kohlmeyer f4d9715cc7
make code follow LAMMPS conventions more closely and do some cleanups 
- remove tabs and trailing whitespace
- remove references to atom style body, since code only works with ellipsoid
- adjust function names and tests for requirements to be more obvious and work correctly in parallel
- remove rather specific debug code
- remove non-essential c++11 features
- refactor, correct, and simplify parsing of types keyword arguments
 2020-01-19 13:07:54 -05:00
Pierre de Buyl 4c8a857960 Merge branch 'master' into fix-active-rebase-5 2020-01-17 22:11:55 +01:00
Axel Kohlmeyer 998b60eabc
restore accidentally renamed keyword 2020-01-17 12:17:47 -05:00
Axel Kohlmeyer a53202bad2
removing the time estimate code for create_atoms completely, as we'll have linear scaling soon. 2020-01-16 17:23:57 -05:00
Axel Kohlmeyer dd60bddc33
reset embedding step counter when init_style() is called 2020-01-16 17:14:23 -05:00
Axel Kohlmeyer 79f9ede38a
print warning when using pair_write on EAM pair style 2020-01-16 16:51:32 -05:00
Axel Kohlmeyer 070bb8c5cd
change estimate for creating atoms after benchmarking a 440M atom system 2020-01-16 16:46:37 -05:00
Axel Kohlmeyer 93a6d3a1fc
print warning (once) if EAM embedding data is out of sync, error out, if embedding term is not available at all. 2020-01-16 16:35:05 -05:00
Axel Kohlmeyer 4dc37bf56e
replace tabs and remove trailing whitespace 2020-01-16 14:06:15 -05:00
Axel Kohlmeyer cf80495a3d
change estimate for time to create an atom from 25ns to 1us 2020-01-16 12:15:42 -05:00
oywg11 b2b28015c4 New ILP paramters 2020-01-16 16:46:04 +02:00
Axel Kohlmeyer f1c79fb914
Merge pull request #1096 from ProfessorMiller/master 
Changes to the NH fix enabling Cauchy stress control (Cauhchystat) du…
 2020-01-15 17:35:03 -05:00
Axel Kohlmeyer 4e32af5d49
Merge branch 'master' into pair-bop-updates 2020-01-15 17:13:22 -05:00
Axel Kohlmeyer 62f0d87e59
update .gitignore for recently added styles 2020-01-15 17:13:14 -05:00
Axel Kohlmeyer 4801f013a5
correct logic error in reading of bop potential files 2020-01-15 16:49:23 -05:00
Axel Kohlmeyer 3efc5b0b64
Merge pull request #1841 from phankl/stable 
Mesoscopic potential for carbon nanotubes
 2020-01-15 16:31:40 -05:00
Axel Kohlmeyer f888c436c3
use safe fgets version and check sscanf() return value for correct parsion of potential file header 2020-01-15 14:24:02 -05:00
Axel Kohlmeyer 3cb26e576d
make sure communication buffers are fully initialized 2020-01-15 13:47:01 -05:00
Axel Kohlmeyer f05175eb1d
properly initialize eflag/vflag and all related properties 2020-01-15 13:42:50 -05:00
Axel Kohlmeyer 500363ab83
move functions in MathExtra namespace to math_extra.h header file 2020-01-15 13:42:14 -05:00
Axel Kohlmeyer a74c3b912b
remove tabs and trailing whitespace, adjust source format to closer match LAMMPS style 2020-01-15 12:54:37 -05:00
Axel Kohlmeyer 2f1e3d8490
Merge branch 'master' into ph-cntmeso 
# Conflicts:
#	doc/src/pairs.txt
 2020-01-15 11:45:14 -05:00
cdt1802 902d772b85 removed harmonic bond and angle from repo 2020-01-15 13:47:51 +00:00
cdt1802 331fff0613 moved files to USER-MISC, added README entry, added examples 2020-01-15 12:07:26 +00:00
cdt1802 9ef984daaa added documentation 2020-01-15 11:04:43 +00:00
Axel Kohlmeyer 133be2132d
Merge remote-tracking branch 'github/junghans-patch-1' into collected-small-changes 2020-01-14 16:57:52 -05:00
Steve Plimpton ceeae57172 enhanced stochastic wall example 2020-01-14 13:20:35 -07:00
Axel Kohlmeyer 50aa52fc9c
replace (evil) tabs with blanks 2020-01-14 15:08:56 -05:00
Steve Plimpton be8832be99 Merge branch 'master' into nparticles 2020-01-14 12:36:02 -07:00
Axel Kohlmeyer b9c6e0f700
Merge pull request #1691 from toquydong/stochasticwall 
Implementation of statistical gas wall boundary conditions
 2020-01-14 14:11:16 -05:00
Axel Kohlmeyer cae994dea9
fix whitespace issues 2020-01-14 13:24:40 -05:00
Axel Kohlmeyer 2f83b32030
Merge branch 'master' into pair-bop-updates 2020-01-14 13:15:05 -05:00
Steve Plimpton 628dc6dd2a sync with master 2020-01-14 10:40:05 -07:00
Steve Plimpton 07e58fd681 document latest fix hyper/local diagnostics 2020-01-14 10:36:19 -07:00
To Quy-Dong 1ce1474864
Update README 2020-01-14 18:13:53 +01:00
To Quy-Dong 9de4e56f3e
Update README 2020-01-14 18:12:33 +01:00
To Quy-Dong 41792da707
Update fix_wall_reflect_stochastic.cpp 2020-01-14 18:08:42 +01:00
Steve Plimpton ea24ec8d6a minor formatting edits 2020-01-14 09:15:05 -07:00
Steve Plimpton 95a3abc74e Merge branch 'master' into fire 2020-01-14 08:53:40 -07:00
Axel Kohlmeyer b308f1c4e0
fix whitespace issue 2020-01-14 10:26:25 -05:00
Axel Kohlmeyer e03b7c5441
Merge branch 'master' into message-iterate 2020-01-14 10:10:08 -05:00
Axel Kohlmeyer 0a84106b23
fix whitespace issues 2020-01-13 22:47:06 -05:00
Philipp Kloza c8f6866f0d fixed minor bug in memory allocation for coefficients 2020-01-13 23:01:20 +00:00
Philipp Kloza 2b51938a94 changed potential file format to single file 2020-01-13 22:52:52 +00:00
Steve Plimpton d3348371e1 refactoring of code and doc files 2020-01-13 15:22:02 -07:00
Steve Plimpton aa70f8cc6b small edits for reformatting 2020-01-13 14:26:22 -07:00
Steve Plimpton 51efee43be sync to master 2020-01-13 13:42:05 -07:00
Steve Plimpton 9ed987c255 minor changes to syntax and documentation of fix deposit orient 2020-01-13 13:15:17 -07:00
cdt1802 afcc1d935d added and corrected error and warning messages 2020-01-13 17:45:38 +00:00
Steve Plimpton e8d11931ec merged in current master 2020-01-13 10:34:31 -07:00
Axel Kohlmeyer 2d28e9fa2e
check for FFT_FFTW_THREADS may only run when CUDA is not enabled 2020-01-13 12:08:46 -05:00
cdt1802 03a7f617eb now opening files with lmp method 2020-01-13 17:05:31 +00:00
Steve Plimpton 99dc283f82 Merge branch 'master' into message-iterate 2020-01-13 09:30:51 -07:00
cdt1802 e35f160e9c added standard potential files to git repo 2020-01-13 16:23:07 +00:00
Axel Kohlmeyer 206aa77532
fix one more whitespace issue 2020-01-13 11:22:42 -05:00
Axel Kohlmeyer 5198058691
fix whitespace issues in fft3d_kokkos files 2020-01-13 11:21:44 -05:00
Axel Kohlmeyer a7720124db
check and adjust FFT selection for KOKKOS depending on whether CUDA is enabled or not 2020-01-13 11:09:37 -05:00
Axel Kohlmeyer 2834965e98
Merge branch 'master' into fft 
# Conflicts:
#	doc/txt/kspace_style.txt
 2020-01-13 10:53:26 -05:00
Axel Kohlmeyer 6813ab4c9c
Merge pull request #1832 from akohlmey/doc-styles-check 
Check style command lists against existing styles in sources
 2020-01-13 10:38:26 -05:00
Axel Kohlmeyer eed85bb676
Merge pull request #1834 from akohlmey/suffix-flag-refactor 
Small Suffix flag refactoring and disallow per substyle special overrides for USER-INTEL and GPU
 2020-01-13 10:37:35 -05:00
cdt1802 8e08acd5d4 moved mesocnt to user packages 2020-01-13 15:01:03 +00:00
cdt1802 9d207e5829 renamed mesocnt directory 2020-01-13 15:00:42 +00:00
cdt1802 b18f79abe0 merged latest stable version into fork 2020-01-13 14:31:18 +00:00
cdt1802 fe1f7f9a9c restored Makefile.g++_openmpi to default 2020-01-13 13:00:31 +00:00
cdt1802 601658fa50 removed unnecessary headers and converted ints for tag and mol to tagint 2020-01-13 12:56:30 +00:00
Axel Kohlmeyer 7cb36d1705
Merge branch 'master' into fft 2020-01-12 20:22:15 -05:00
Axel Kohlmeyer 22af416c53
correct output to be consistent with other code in LAMMPS 2020-01-12 14:47:15 -05:00
Axel Kohlmeyer 0d6ec02d5a
small corrections and more cleanup 2020-01-12 14:31:05 -05:00
Axel Kohlmeyer 107c5bbced
Merge branch 'master' into cauchystat and resolve conflicts 
# Conflicts:
#	cmake/CMakeLists.txt
#	doc/src/Commands_fix.txt
#	doc/src/Packages_details.txt
#	doc/src/Packages_user.txt
#	doc/src/fix_nh.txt
#	doc/src/fixes.txt
#	doc/src/lammps.book
#	src/Makefile
 2020-01-12 13:58:41 -05:00
Axel Kohlmeyer b6d86e3c91
merge fix sources and move into USER-MISC package. clean up docs 2020-01-12 13:45:22 -05:00
Axel Kohlmeyer ef4e061cb7
merge contents of fix_npt_cauchy files into fix_cauchy 2020-01-12 13:27:40 -05:00
Axel Kohlmeyer 9811a85a9a
reformat 2020-01-12 13:09:53 -05:00
Axel Kohlmeyer a957d1c4c2
fix whitespace issue 2020-01-11 21:05:08 -05:00
Axel Kohlmeyer cb8313d947
document added warning for fix bond/create 2020-01-11 16:08:37 -05:00
Axel Kohlmeyer 9ed9b4338b
fix several memory leaks in pair style bop exposed when using the pair_coeff command multiple times 2020-01-11 14:03:30 -05:00
cdt1802 869e2f0916 added support for all unit styles except lj 2020-01-11 16:32:00 +00:00
Steve Plimpton 8fa0700df1 add warning to fix bond/create 2020-01-10 16:49:09 -07:00
Axel Kohlmeyer d0eb41b61e
disallow per substyle special bond factors with certain suffix styles 2020-01-10 16:58:39 -05:00
Axel Kohlmeyer 4989c3a878
convert static const ints to an enumerator 2020-01-10 15:30:26 -05:00
Axel Kohlmeyer f073a64549
add suffix_flag settings to GPU package styles 2020-01-10 15:29:53 -05:00
Pierre de Buyl fe4f7899d2 Use x-axis along the particle's quaternion. 
This change allows the fix to work in 2D as well.
 2020-01-10 11:32:57 +01:00
Stefan Paquay 60c0270375 Added option to impose fix propel/self only to specific types 2020-01-10 11:32:03 +01:00
Stefan Paquay 768fd8f7fe Added type support. 2020-01-10 11:32:02 +01:00
Stefan Paquay 3144b91fb3 Some code clean-up, added safety check in post_force_velocity. 2020-01-10 11:31:58 +01:00
Stefan Paquay 074dfd8651 Commit before merging latest changes in master. 2020-01-10 11:31:57 +01:00
Stefan Paquay 8c7890b6df Added two modes, one via velocity and one via quaternion. 2020-01-10 11:31:57 +01:00
Stefan Paquay 942812a654 Commit before changing branches. 2020-01-10 11:31:21 +01:00
Stefan Paquay 2a0081d135 Renamed fix active to fix propel/self 2020-01-10 11:31:20 +01:00
Stefan Paquay c93ca5b4a4 Added a fix to add active force to particles. 2020-01-10 11:31:16 +01:00
Stefan Paquay 5139f3af33 Fixed compile error for fix_momentum_kokkos. 2020-01-10 11:17:37 +01:00
Stefan Paquay 7af38e0862 Makefile.kokkos_cuda_mpi 2020-01-10 11:17:37 +01:00
Stefan Paquay 4853b43f16 Commit change in fix_wall_region before merge. 2020-01-10 11:17:37 +01:00
jrgissing 683d6ce9b3 'install' USER-REACTION package 2020-01-09 21:11:30 -07:00
jrgissing c3922c7e35 rename package USER-REACTION 2020-01-09 20:07:41 -07:00
cdt1802 c06ba2b295 moved matrix functions into separate MathExtra namespace in pair_mesocnt.h 2020-01-09 09:28:35 +00:00
Axel Kohlmeyer 514271c984
recover compilation with -DLAMMPS_BIGBIG and fix whitespace and formatting issues 2020-01-08 17:57:54 -05:00
Axel Kohlmeyer c482a04f80
fix whitespace issue 2020-01-08 17:21:35 -05:00
Axel Kohlmeyer a3fd7345a7
Merge branch 'master' into next_patch_version 2020-01-08 17:20:36 -05:00
Axel Kohlmeyer 2d71d9d47b
add citation for GPU accelerated TIP4P style 2020-01-08 16:15:18 -05:00
Axel Kohlmeyer 6e2c3b7ce9
Merge branch 'master' into collected-small-fixes 2020-01-08 16:14:19 -05:00
Axel Kohlmeyer 481c647889
Merge pull request #1776 from Vsevak/tip4p_gpu 
GPU support for lj/cut/tip4p/long pair style
 2020-01-08 15:35:39 -05:00
Axel Kohlmeyer 9e3364ed39
no need to flag ibody as private 2020-01-08 15:13:34 -05:00
Axel Kohlmeyer 7051c941e5
Merge branch 'master' into collected-small-fixes 2020-01-08 15:05:03 -05:00
Axel Kohlmeyer c5768acbbc
Merge pull request #1801 from lammps/rigid-gravity 
enable fix rigid commands to add gravity to COM of rigid bodies
 2020-01-08 14:47:03 -05:00
Axel Kohlmeyer e243ca92b0
step version string for next patch release 2020-01-08 14:31:08 -05:00
cdt1802 a9a033de6f adjusted formatting 2020-01-08 15:39:55 +00:00
Axel Kohlmeyer 1cd6d302bb
Merge pull request #1823 from dsbolin/rigid-gravity 
Adds an example using new options in fix rigid and fix gravity
 2020-01-08 09:15:55 -05:00
cdt1802 4599ffd4d5 removed numerical integration, cleaned up file 2020-01-08 13:28:00 +00:00
cdt1802 a219e442f4 swapped newton off to newton on - now working in parallel 2020-01-08 10:31:00 +00:00
tabedzki2 f1a23b1ea2
Updated Makefile.stampede: replacement options icc 
The default options for Makefile.stampede did not compile. They had to be updated to include the `q` replacement options.
 2020-01-07 21:47:43 -05:00
Vsevak e8a941a0b9 Remove unnecessary data transfer from tip4p/gpu pairstyle init 
Such data transfer is performed at each timestep, so it does not belong to the initialization
 2020-01-08 01:48:47 +03:00
Axel Kohlmeyer 23b73a0ebc
plug small memory leak 2020-01-07 15:32:44 -05:00
Axel Kohlmeyer f8ad7cc90f
refactor fix for detecting intel pair styles in hybrid pair styles 2020-01-07 15:09:50 -05:00
Axel Kohlmeyer 4c974c6d5e
avoid uninitialized memory access when used with hybrid styles 2020-01-07 11:14:22 -05:00
Axel Kohlmeyer 7470a120bb
fix small memory leak in USER-INTEL binning style 2020-01-07 11:13:43 -05:00
Axel Kohlmeyer 5500198b4e
correct whitespace issue in dynamical_matrix.cpp 2020-01-06 15:21:18 -05:00
Axel Kohlmeyer 394e5459b6
correct whitespace issues in pair_meamc.cpp 2020-01-06 15:16:08 -05:00
Axel Kohlmeyer fbc0b8a881
Merge branch 'master' into collected-small-fixes 2020-01-06 15:14:48 -05:00
Axel Kohlmeyer 00dfde2952
Merge pull request #1783 from ares201005/fix_dynmat 
add force modifications in dynamical_matrix.cpp
 2020-01-06 15:08:35 -05:00
Axel Kohlmeyer 1be8109618
Merge pull request #1798 from martok/meamc-dec19 
Collected MEAM/C additions
 2020-01-06 15:07:08 -05:00
cdt1802 abb1b6bab4 added full p1,p2 swap for CNT end at end of chain 2020-01-06 13:20:41 +00:00
cdt1802 949337abff numerical differentiation for r1,r2, fixed bug in end indices and added p1,p2 swap for r1,r2 forces 2020-01-06 11:33:58 +00:00
cdt1802 a145e5cd3c fixed bug in forces acting on chain 2020-01-04 17:47:38 +00:00
Axel Kohlmeyer a63792a07a
need to explicitly run pair_init_check() inside kspace_init_check() for hybrid styles 2020-01-03 01:40:20 -05:00
Axel Kohlmeyer 2f6018b099
use regex pattern matching to make style lookup more specific with less code 2020-01-03 01:39:35 -05:00
Axel Kohlmeyer e11374d433
print intel package status message only once per run 2020-01-03 01:37:12 -05:00
jrgissing a36acf5547 USER-REACT readme 2020-01-01 13:07:46 -05:00
jrgissing 96fb374641 bond/react: create USER-REACT 2020-01-01 13:04:59 -05:00
cdt1802 c28a9704e2 changed output format for time averaged values 2019-12-30 16:25:30 +00:00
cdt1802 9239688b8f added correct force expressions for approximate chain 2019-12-30 16:24:39 +00:00
cdt1802 ed1d633060 added harmonic bond and angle to commit 2019-12-23 14:50:14 +00:00
cdt1802 309936027b added harmonic bond and angle to commit 2019-12-23 14:49:44 +00:00
cdt1802 e34234d07b fixed bug with empty neighbor lists 2019-12-23 12:08:58 +00:00
cdt1802 200b539d09 added forces on CNT chain 2019-12-22 09:55:40 +00:00
Axel Kohlmeyer 2084d0657a
Merge branch 'fft' of github.com:stanmoore1/lammps into fft 
# Conflicts:
#	doc/src/Build_settings.txt
#	src/KOKKOS/fft3d_kokkos.cpp
 2019-12-21 11:09:16 -05:00
cdt1802 5268ceaf08 initial commit 2019-12-21 12:36:20 +00:00
Axel Kohlmeyer a88a00dbbb
remove trailing whitespace 2019-12-20 15:08:51 -05:00
Axel Kohlmeyer 3b76ab56f0
port gravity changes to rigid fixes to USER-OMP package versions 2019-12-20 12:09:50 -05:00
cdt1802 3631a50b83 cleaned up indents 2019-12-20 11:24:44 +00:00
Steve Plimpton a11b886b5c add warning if gravity is used incorrectly with overlapped rigid bodies 2019-12-19 16:17:14 -07:00
Axel Kohlmeyer 402f5585ff
Merge pull request #1795 from jrgissing/bond/react-chiral_centers 
Bond/react chiral centers
 2019-12-19 16:13:32 -05:00
Axel Kohlmeyer 5a2074cc5a
Merge pull request #1816 from stanmoore1/kk_min_fix 
Fix issue in Kokkos minimize
 2019-12-19 16:12:53 -05:00
Axel Kohlmeyer 27180e0b22
Merge pull request #1812 from ohenrich/user-cgdna 
USER-CGDNA: Added oxRNA2 files to .gitignore
 2019-12-19 14:58:56 -05:00
Jianhua Pan 92b2e4256b
Bug fix for lj/class2/coul/long/gpu 2019-12-19 14:45:19 -05:00
Stan Moore 7d16783366 Fix issue in Kokkos minimize 2019-12-19 09:31:30 -07:00
Oliver Henrich d05f32d152 Added oxRNA2 files to .gitignore 2019-12-18 11:31:02 +00:00
Michael Brown 3be04e4671 Bug fix for USER-INTEL package with triclinic neighbor builds. 2019-12-18 01:27:39 -08:00
Bryce Adelstein Lelbach aka wash b90c372a63 Fix mismatches in CUDA execution space qualifiers between declarations and 
definitions.

Add missing `KOKKOS_INLINE_FUNCTION` to the definition of:
- `FixEnforce2DKokkos::post_force_item`
- `FixNeighHistoryKokkos::zero_partner_count_item`
- `FixNeighHistoryKokkos::pre_exchange_item`

Add missing `KOKKOS_FUNCTION` to the definition of:
- `NeighborKokkosExecute::build_Item`
- `NeighborKokkosExecute::build_Item_Ghost`
- `NeighborKokkosExecute::build_ItemSize`
 2019-12-17 17:27:51 -08:00
Sebastian Hütter cb20cb9f25 Add range checks for MathSpecial::fm_exp 2019-12-17 22:23:19 +01:00
Sebastian Hütter a231197c10 MEAM/C: remove unused variable alias 2019-12-17 21:55:50 +01:00
Stan Moore 4c9d355fc7 Fix compile error in fft3d_kokkos.cpp 2019-12-16 13:30:52 -07:00
Axel Kohlmeyer 55fde76d59
may only close files on MPI ranks that have a file reader instance 2019-12-16 07:22:41 -05:00
Stan Moore c169e88268 Update from master 2019-12-13 16:42:05 -07:00
Richard Berger 6c3161cb55
Merge pull request #1796 from athomps/compute-snap-tweak 
Fixed error in compute snap for quadratic and add log files for regre…
 2019-12-13 11:55:20 -07:00
Richard Berger 8030ff255d
Merge pull request #1794 from yafshar/master 
Certificate Verification
 2019-12-12 13:24:21 -07:00
Yaser Afshar b0d0037f50 Certificate Verification 
if SSL report an error ("certificate verify failed") during the
handshake and thus refuses further communication with that server,
you can specify your own CA cert path by setting the environment
variable CURL_CA_BUNDLE to the path of your choice.
 2019-12-12 12:57:34 -06:00
Richard Berger a1e49eced7
Merge pull request #1806 from akohlmey/mpi-info-in-help 
Include MPI version and vendor info in LAMMPS help message
 2019-12-12 09:37:28 -07:00
Richard Berger 96f75c7b67
Merge pull request #1802 from rbberger/small-fixes 
Collection of small fixes
 2019-12-12 09:36:53 -07:00
Richard Berger 5e4e6b2853
Merge pull request #1803 from stanmoore1/kk_mpi 
Fix performance issues with CUDA-aware MPI
 2019-12-11 13:34:33 -07:00
Axel Kohlmeyer 5e983b899a
remove unused variable 2019-12-11 08:34:56 -05:00
Axel Kohlmeyer 876032b762
refactor MPI library info query so it can be added to -help flag output 2019-12-11 05:33:16 -05:00
Dan S. Bolintineanu af4e49a517 Merge branch 'rigid-gravity' of github.com:lammps/lammps into rigid-gravity 2019-12-10 14:14:21 -07:00
Stan Moore fba97b94cb Don't change comm flags when there is only 1 MPI rank 2019-12-10 10:10:12 -07:00
Oliver Henrich bf1ee20403 Added oxRNA2 files to Install.sh script 2019-12-10 14:46:24 +00:00
Stan Moore 1b9214c3e9 Fix issues with CUDA-aware MPI 2019-12-09 15:21:47 -07:00
Richard Berger 00547d906b Fix whitespace 2019-12-06 14:43:45 -05:00
Richard Berger e68824a392
Merge pull request #1772 from ohenrich/user-cgdna 
USER-CGDNA oxRNA2 Implementation
 2019-12-06 12:23:47 -07:00
Vsevak a2f9fa8e78 Separate the computation of hneigh into another kernel 
Simplify the main GPU kernel and add another kernel 'k_pair_reneigh'. It works good on GTX1070 (Pascal), but still there is a problem with non-deterministic results on Volta.

I reimplement BaseCharge::compute methods in the child class LJ_TIP4PLong to correctly embed a new kernel in the code.

Also commit includes some codestyle fixes.
 2019-12-06 21:41:02 +03:00
Steve Plimpton 5859b18d2f enable fix rigid commands to add gravity to COM of rigid bodies 2019-12-06 11:04:50 -07:00
Sungkwang Mun 81fb0d613f * This commit includes the addition of new reference structures such as 
ch4: methane-like structure only for binary system.
dia3: diamond structure with primary 1NN and secondary 3NN inteation
tri: H2O-like structure that has an angle
zig: zigzag structure with a uniform angle
lin: linear structure (180 degree angle)

** tri, zig, and lin reference structures require angle information (in degree)
such as the following.
   theta = 109.5
 2019-12-03 19:36:35 +01:00
Richard Berger e08ba3f11e Merge branch 'master' into library_interface_update 2019-12-03 12:51:17 -05:00
Sebastian Hütter ce05ed4cca MEAM/C: infer z parameter from lattice structure, eliminates possible user mistakes 2019-12-03 18:06:34 +01:00
Sebastian Hütter 7e14dda789 MEAM/C: warn if z given and expected by lattice do not agree 2019-12-03 18:06:29 +01:00
Sebastian Hütter 2c65659421 MEAM/C: implement scaling factor for reversible scaling calculations 2019-12-03 18:06:29 +01:00
Sebastian Hütter 204529bcaf MEAM/C: remove unused vars, refactoring for extensibility 2019-12-03 18:06:29 +01:00
Sebastian Hütter cd6d2c55d1 MEAM/C: helper function for x=1 2019-12-03 18:06:29 +01:00
phankl 1172f7bd96
Delete pair_mesocnt_old.h 
deleted old implementation files
 2019-12-03 13:25:31 +00:00
phankl 6da8a4ca1e
Delete pair_mesocnt_old.cpp 2019-12-03 13:25:07 +00:00
Aidan Thompson 7233c3fedf Fixed error in compute snap for quadratic and add log files for regression testing 2019-12-02 18:30:38 -07:00
jrgissing 4cb797e63d correct image atom mistake 2019-12-02 14:25:58 -05:00
jrgissing 819fe9ec56 add option to enforce atom chirality 2019-12-02 12:27:57 -05:00
cdt1802 93eb518f5d made local neighbor list, updated when regular list is updated leading to speed-up 2019-12-02 16:54:35 +00:00
Richard Berger 1d92840918
Merge pull request #1792 from akohlmey/library-define-fix 
Improve handling of LAMMPS integer size defines in library.h
 2019-12-02 08:48:34 -07:00
jrgissing 36e102516f angle constraint bugfix 
ghost atom fix
 2019-12-02 10:34:03 -05:00
cdt1802 f801fbaca1 outsourced parts of compute into separate functions 2019-12-02 12:45:32 +00:00