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6990 Commits

Author SHA1 Message Date
Axel Kohlmeyer c3f6e27bfe augment documentation for newly added multi-threaded reax/c styles 2017-05-25 17:00:19 -04:00
Axel Kohlmeyer 0a2fe70511 remove redundant code from fix qeq/reax and qeq/reax/omp 2017-05-25 16:31:31 -04:00
Axel Kohlmeyer 53e7fee5b7 Merge branch 'doc-fixes' of github.com:akohlmey/lammps into doc-fixes 2017-05-25 10:11:31 -04:00
Axel Kohlmeyer 5291f2ed6e fix bug in fix shear/history reported by kevin hanley. see #500 2017-05-25 10:11:24 -04:00
Axel Kohlmeyer 99a68e487f fix suffix style handling bug for adding fixes and computes 2017-05-25 02:01:04 -04:00
Axel Kohlmeyer 271431ab18 clean up code so it can be compiled with and without OpenMP enabled regardless of whether the USER-OMP package is installed 2017-05-24 17:25:57 -04:00
Axel Kohlmeyer 88d4150d2b remove trailing whitespace 2017-05-24 16:29:56 -04:00
Axel Kohlmeyer 0e3cfbc007 remove trailing whitespace 2017-05-24 16:29:26 -04:00
Axel Kohlmeyer 5345ad2da7 merge in the remainder of the USER-REAXC-OMP code. still a lot of work to do. compiles only with -fopenmp active 2017-05-24 16:24:43 -04:00
Axel Kohlmeyer bb890941ca first chunk of code from USER-REAXC-OMP imported and adapted into USER-REAXC 2017-05-24 00:19:36 -04:00
Axel Kohlmeyer 4002dce639 restore explicit NAN constants in output 2017-05-22 22:39:52 -04:00
Axel Kohlmeyer c801cdd81f some more formatting cleanup in fix neb 2017-05-22 22:33:14 -04:00
Axel Kohlmeyer 9008a31190 more formatting cleanup 
This cleans up and simplifies the neb command code some more
 2017-05-22 21:55:55 -04:00
Richard Berger bdfb7c69ea Remove unused code detected by coverity CID 177700 2017-05-22 17:51:40 -04:00
Richard Berger 084626e60b Fixes coverity issue CID 179426 2017-05-22 17:36:16 -04:00
Richard Berger a7d790a827 Fixes coverity issue CID 179439 2017-05-22 17:33:47 -04:00
Richard Berger 8a630ff4ec Fixes coverity issue CID 179440 2017-05-22 17:32:07 -04:00
Richard Berger 617ca4e0c8 Fixes coverity issue CID 179436 2017-05-22 17:30:46 -04:00
Axel Kohlmeyer 62601678cd when growing arrays with reallocate, always check against atom->nmax and not atom->nlocal or else these arrays may be of inconsistent size and communication can lead to data corruption 2017-05-22 17:16:19 -04:00
Axel Kohlmeyer 081910adbc do not try to free null communicators 2017-05-22 17:15:14 -04:00
Axel Kohlmeyer f73fd0625d rename nall class member to numall to avoid confusion with the common convention nall = atom->nlocal+atom->nghost 2017-05-22 17:14:38 -04:00
Axel Kohlmeyer 7185db98b4 NEBLongRange was incorrectly set to false by default. revert to true. 2017-05-22 17:13:38 -04:00
Axel Kohlmeyer 4780d72809 use '&&' and '||' instead of 'and' and 'or' operators for consistency 2017-05-22 14:42:42 -04:00
Axel Kohlmeyer 3fd91a239f avoid use '&&' and '||' instead of 'and' and 'or' for consistency 2017-05-22 14:41:01 -04:00
Axel Kohlmeyer 546aed7ccd plug some memory leaks 2017-05-19 16:14:59 -04:00
Axel Kohlmeyer 6ef79d3715 silence several compiler warnings 2017-05-19 15:13:19 -04:00
Axel Kohlmeyer c2bf3269ac formatting cleanup. combine 8 MPI_Allreduce() calls into 1 2017-05-19 15:02:29 -04:00
Steve Plimpton 2225fce94e patch 19May17 2017-05-19 07:35:36 -06:00
Emile Maras 069f3e746b small formating changes 2017-05-18 21:23:29 +02:00
Steve Plimpton b28ecd44c2 update docs before patch release 2017-05-18 13:14:47 -06:00
sjplimp 9db9fc9de3 Merge pull request #491 from akohlmey/fix-bigint-thermo-in-variables-bug 
convert bigint values for bonds/angles/dihedrals/impropers to doubles
 2017-05-18 13:08:42 -06:00
sjplimp 6ac9b7a1b0 Merge pull request #482 from akohlmey/add-pair-python 
Add python pair style for implementing simple pairwise additive potentials in python
 2017-05-18 11:15:58 -06:00
Axel Kohlmeyer 34dbf6b225 do not compute properties twice 2017-05-18 12:45:43 -04:00
Axel Kohlmeyer 26d71b66e4 convert bigint values for bonds/angles/dihedrals/impropers to doubles when evaluating those keywords in variable expressions 2017-05-18 12:41:48 -04:00
Richard Berger 65eacb6b90 Fix compilation warnings in fix_python 2017-05-18 12:20:39 -04:00
sjplimp cb3344a337 Merge pull request #489 from akohlmey/thread-safe-biasing 
port thread-safe temperature biasing from LAMMPS-ICMS
 2017-05-18 09:15:07 -06:00
sjplimp 5d38cbbce9 Merge pull request #487 from akohlmey/pair_edip_multi_element 
Import multi-element compatible pair style edip as edip/multi
 2017-05-18 09:13:30 -06:00
sjplimp 30babd8157 Merge pull request #485 from akohlmey/pair_settings_cut_bugfix 
Bugfix for correct resetting of previously set cutoffs to various Pair::settings() functions
 2017-05-18 09:12:47 -06:00
sjplimp aa09f45b7e Merge pull request #484 from akohlmey/add-gao-weber-styles 
Add Gao-Weber manybody styles
 2017-05-18 09:10:03 -06:00
sjplimp 4b61cf6f52 Merge pull request #483 from akohlmey/airebo-spline-bugfix-refactor 
AIREBO spline code out-of-bounds and bondorder derivative bugfix and refactor
 2017-05-18 09:01:33 -06:00
sjplimp 683f3d9d2a Merge pull request #481 from akohlmey/collected-small-changes 
Collected small updates and bugfixes
 2017-05-18 09:01:04 -06:00
sjplimp ce18524251 Merge pull request #480 from akohlmey/pair_morse_smooth_linear_bugfix 
corrections to pair style morse/smooth/linear
 2017-05-18 08:57:24 -06:00
Emile Maras 8daba01151 some small formating change but does not work anymore 2017-05-18 16:48:20 +02:00
Emile Maras 640edbc1d4 added several features to the NEB 2017-05-18 11:08:08 +02:00
Axel Kohlmeyer 4b1914aa1f update citations for multi-element edip potential 2017-05-18 01:07:52 -04:00
Axel Kohlmeyer 67962b15fc a bunch refactoring changes in the python pair style and the examples 
- make all python potential classes derived from LAMMPSPairPotential
  which contains shared functionality. We currently don't check
  for supported atom types. may want to add that again later.
- keep track of skipped atom types in the C++ code.
- add test against units setting. must set self.units='...' in constructor
- make compute_force method consistent with Pair::single() in LAMMPS and return force/r instead of force.
- rename potentials.py to py_pot.py
- update test runs. some small tweaks.
 2017-05-17 20:55:48 -04:00
Axel Kohlmeyer 43efe9e417 adding Pair::single() support to python pair style and examples 
with the single function, python pair styles can be massively
sped up and made compatible to accelerators, as one can translate
the analytic force and energy functions through LAMMPS into suitable
tables and then simply use the on-the-fly tables for production runs
 2017-05-17 17:20:56 -04:00
Axel Kohlmeyer 278b9f7fba move pair gw and gw/zbl to USER-MISC package 2017-05-17 14:59:46 -04:00
Axel Kohlmeyer 45becfb235 correct author attributions 2017-05-17 09:59:01 -04:00
Richard Berger 7caf6cf459 Change how a Python pair style is loaded 
Implements a class loader which takes a fully qualified Python class
name, loads the module and creates an object instance.

To add flexibility, the current working directory and the
directory specified by the LAMMPS_POTENTIALS environment variable are
added to the module search path.
 2017-05-16 23:29:48 -04:00
Axel Kohlmeyer d2810f9f83 port thread-safe temperature biasing from LAMMPS-ICMS 2017-05-16 18:15:13 -04:00
Steve Plimpton 7f9a331c73 bugfix for 2 recenty reported neighbor issues, also a ReaxFF fix species issue 2017-05-16 15:51:41 -06:00
Axel Kohlmeyer 35e92733e9 import multi-element compatible pair style edip as edip/multi 2017-05-16 17:40:59 -04:00
Axel Kohlmeyer c11e87618b implement second bugfix suggestion from @CF17 on issue #59 2017-05-16 14:18:56 -04:00
Axel Kohlmeyer ca87e57129 improved version of AIREBO splines based on a suggestion by markus hoehnerbach 2017-05-16 11:58:34 -04:00
Axel Kohlmeyer d807ba1974 whitespace cleanup 2017-05-16 00:26:39 -04:00
Axel Kohlmeyer 51fc386e72 correct the inner loop range for resetting cutoffs when redefining a pair style 
this was reported by frank uhlig on lammps-users for lj/cut, but it applies to many more pair styles
 2017-05-16 00:26:18 -04:00
Richard Berger a6f0d700f1 Merge branch 'add-pair-python' of github.com:akohlmey/lammps into add-pair-python 2017-05-15 18:44:52 -04:00
Axel Kohlmeyer d66a696a84 avoid preprocessor warnings, by placing Python.h include file on the top, as suggested by python docs 2017-05-15 18:02:02 -04:00
Richard Berger 69ccbd1562 Extract common wrappers to Python compatibility header 2017-05-15 17:46:57 -04:00
Axel Kohlmeyer d9d4ef17c8 add gao-weber potentials (regular and with ZBL core) with SiC potential files 
NOTE: documentation is missing
 2017-05-15 17:44:25 -04:00
Axel Kohlmeyer 0a40a7af7b whitespace cleanup 2017-05-15 17:00:41 -04:00
Axel Kohlmeyer eb6f6a77e5 dead code removal 2017-05-15 16:16:12 -04:00
Axel Kohlmeyer fb7164a811 replace pow(x,-0.5) with 1.0/sqrt(x) 2017-05-15 16:16:01 -04:00
Axel Kohlmeyer 64cf52d3b5 address spline out-of-bounds bug reported in issue #59 and refactor high-level spline code for consistency and efficiency 2017-05-15 15:55:15 -04:00
Axel Kohlmeyer d662f5d429 whitspace cleanup and gitignore update 2017-05-15 00:22:22 -04:00
Axel Kohlmeyer 6e113c1eaf basic feature complete version of lj melt example with python interaction function 2017-05-15 00:15:41 -04:00
Axel Kohlmeyer 34cc3946b8 first few pieces of pair style python 2017-05-14 18:29:06 -04:00
Axel Kohlmeyer 6aa0250bc5 corrections to pair style morse/smooth/linear contributed by David R. Heine 2017-05-12 23:40:24 -04:00
Richard Berger c4d0f07093 Allow fix python to only execute every N steps 2017-05-12 00:29:58 -04:00
Richard Berger 110bb79b14 Implement fix python mentioned in issue #454 
Allows to call a python function at defined points in the integration loop
 2017-05-11 23:50:30 -04:00
Axel Kohlmeyer d84f8898b7 implement functions to execute arbitrary python code from strings or files and recast the python source keyword through using them. 2017-05-11 22:39:08 -04:00
Axel Kohlmeyer 27a6371f9b implement a `python source` command as suggested in issue #454 2017-05-11 19:18:09 -04:00
sjplimp a069d21621 Merge pull request #476 from akohlmey/dump_custom_bugfix 
dump custom memory allocation bugfix
 2017-05-11 09:27:08 -06:00
sjplimp d7f54464c6 Merge pull request #474 from rbberger/dump_vtk_fixes 
Various dump vtk fixes
 2017-05-11 09:25:42 -06:00
sjplimp 998eb44e83 Merge pull request #473 from akohlmey/compress-for-reaxc-fixes 
compressed output via gzip for some ReaxFF fixes
 2017-05-11 09:25:18 -06:00
sjplimp 96d1de8575 Merge pull request #471 from akohlmey/fix-4may2017-issues 
Fix a bunch of remaining issues in the 4 may 2017 release
 2017-05-11 09:24:35 -06:00
sjplimp deff6ffaac Merge pull request #466 from DallasTrinkle/meam-spline-multicomponent 
Meam spline multicomponent
 2017-05-11 09:22:25 -06:00
Axel Kohlmeyer 328ef873d8 fix mixed memory alloc bug in dump custom. this closes #475 2017-05-10 22:41:41 -04:00
Richard Berger c4ac5773cb Fix segmentation fault in dump vtk 2017-05-10 19:51:14 -04:00
Richard Berger cac1bf83ef Work around VTK 7 API change 2017-05-10 19:41:48 -04:00
Axel Kohlmeyer abeb1e096a add support for gzip compressed output to fix reax/bonds, reax/c/bonds and reax/c/species 2017-05-10 11:19:18 -04:00
Axel Kohlmeyer 9f7ce39f9f correct some more omitted updates 2017-05-09 18:14:34 -04:00
Axel Kohlmeyer 3f4aee1046 implement overlooked changes from 4may2017 patch 2017-05-09 15:57:35 -04:00
Axel Kohlmeyer 390ceb1475 whitespace cleanup 2017-05-09 15:49:37 -04:00
Axel Kohlmeyer 6c5edf6c70 performance improvement through avoiding function call and dereference overhead 
- make i_to_potl() and ij_to_potl() functions inline and const
- don't dereference inside the functions, but cache, if possible in external variables
=> up to 15% speedup.
 2017-05-09 15:38:10 -04:00
Axel Kohlmeyer 9cd994f57c fix issues with potential file parser 
- use Force::open_potential()
- replace ftell()/fseek() with rewind()/fgets() which is safer on windows and other platforms with automatic CR/LF to LF conversion on text files
- make parser use properly NULL terminated strings through using strtok()
 2017-05-09 15:35:48 -04:00
Steve Plimpton 08ec55743e neighbor list bugfix to prevent cycle in copy lists 2017-05-09 08:55:18 -06:00
Richard Berger f8af7edf92 Merge remote-tracking branch 'upstream/master' into python_refactoring 2017-05-06 16:00:22 -04:00
Steve Plimpton a73402ad93 update src/Purge.list with renamed reaxc src files 2017-05-04 14:53:08 -06:00
Steve Plimpton d7dbff0f54 jive Kokkos/reaxc file names with new user-reaxc file names 2017-05-04 14:46:59 -06:00
DallasTrinkle 42531389df Cleanup of style (removing all tabs, shortened long lines). 2017-05-04 15:28:11 -05:00
DallasTrinkle f7230006fe OpenMP version added. 2017-05-04 15:08:04 -05:00
DallasTrinkle 754b40cb31 Removed unused functions. 2017-05-04 13:16:46 -05:00
DallasTrinkle ffdc8b556d Cleanup. 2017-05-04 13:03:09 -05:00
DallasTrinkle 5accce976a Cleanup. 2017-05-04 13:02:09 -05:00
DallasTrinkle 349c1443a1 Cleanup. 2017-05-04 13:01:45 -05:00
DallasTrinkle 2f71245d82 Removed extra "helper" functions. 2017-05-04 13:00:06 -05:00
Steve Plimpton 51c6d50268 patch 4May17 2017-05-04 11:46:58 -06:00
sjplimp 6499cfcf52 Merge pull request #458 from stanmoore1/kokkos_sync_bugfix 
Fixing auto_sync logic bug in modify_kokkos
 2017-05-04 11:24:11 -06:00
sjplimp f08e206991 Merge pull request #457 from stanmoore1/kokkos_ubuf 
Adding ubuf union to Kokkos atom_vec styles
 2017-05-04 11:23:55 -06:00
sjplimp dcc5472cba Merge pull request #452 from akohlmey/small-fixes-and-updates 
Small fixes and updates
 2017-05-04 11:23:23 -06:00
Steve Plimpton addd87c0f7 new Section package and start doc pages and build scripts 2017-05-04 11:22:20 -06:00
DallasTrinkle 480727815a Starting to refactor in preparation to contruct OMP version. 2017-05-04 11:27:55 -05:00
DallasTrinkle 45187a0fc7 Fix system header #include style. 2017-05-04 11:05:50 -05:00
DallasTrinkle 7409c6d781 Cleaned up atom->x and atom->f deferences. 2017-05-03 16:56:07 -05:00
DallasTrinkle 11cb0212b7 Cleanup: two space indent + no trailing spaces on lines. 2017-05-03 16:49:43 -05:00
Axel Kohlmeyer 7f49ee8fd7 print warning about minimization energy with fix box/relax 2017-05-03 15:33:22 -04:00
Stefan Paquay 7adc7f02e0 Stopped working on gaussian bump. 2017-05-03 11:21:18 -04:00
DallasTrinkle 50c7234f26 Fix to communication for mpi. Tested, and now working correctly with MPI. 2017-05-02 09:43:57 -05:00
DallasTrinkle f58fc9488f Fixed neighbor list building that caused error in parallel runs with pair_meam_spline. 2017-05-01 21:56:19 -05:00
DallasTrinkle 408cc19885 Fix for seg fault. 2017-05-01 20:36:09 -05:00
DallasTrinkle c76d27373e Another fix for seg fault in parallel allocation. 2017-05-01 20:33:07 -05:00
DallasTrinkle fb08dc09f3 Small error in elements allocation causing seg. fault for parallel runs; fixed. 2017-05-01 13:38:37 -05:00
Anders Hafreager 914848433a Using correct value for atom->nlocal 2017-05-01 00:02:57 +02:00
DallasTrinkle 8cc8441367 Cleanup on pair_meam_spline.cpp 2017-04-28 14:53:25 -05:00
DallasTrinkle 7d9670bc6c Addition of potential, code modifications to incorporate multicomponent spline MEAM in pair_meam_spline. 
Backwards compatible with previous version of pair_meam_spline.
 2017-04-28 14:48:34 -05:00
Axel Kohlmeyer cd435c0c58 change references from cg_cmm to lj_sdk and from cmm to sdk 2017-04-26 19:44:25 -04:00
Axel Kohlmeyer 548c589f82 update the README for USER-CGSDK 2017-04-26 19:35:54 -04:00
Axel Kohlmeyer 5c7a631988 rename USER-CG-CMM folder to USER-CGSDK 2017-04-26 19:29:39 -04:00
Axel Kohlmeyer 3e60f79f1d remove cg/cmm style name aliases 2017-04-26 17:24:25 -04:00
Anders Hafreager 67fced37c8 Setting molecule COM to 0 after moving atoms 2017-04-26 20:10:18 +02:00
Stan Moore 0565b1df5f Fixing auto_sync logic bug in modify_kokkos 2017-04-26 10:49:20 -06:00
Stan Moore d73d70fa1f Adding ubuf union to Kokkos atom_vec styles 2017-04-26 08:15:42 -06:00
Axel Kohlmeyer ddc1e4e86e detect and refuse to run pair style srp together with fix rigid 2017-04-25 13:27:20 -04:00
Axel Kohlmeyer 2e1f8b4aef make Python::init() method public and remove the now redundant Python::request() method 2017-04-25 10:21:02 -04:00
Giacomo Fiorin 958f05a6f3 Allow requesting Python interpreter without having to define a function just for that 2017-04-25 01:09:05 -04:00
Axel Kohlmeyer 0ac22e034c turn errors from manybody potentials for */tally computes into warnings 2017-04-22 21:50:27 -04:00
Axel Kohlmeyer 197ce4580b avoid division by zero also for ewald/disp 2017-04-21 17:27:08 -04:00
Axel Kohlmeyer 8f14511831 avoid division by zero by initializing unset (=automatic) g_ewald parameters to some number > 0. 2017-04-21 16:46:27 -04:00
Axel Kohlmeyer 4e411364ff add support to pair_modify to selectively disable compute/tally callbacks in sub-styles for pair hybrid and hybrid/overlay 2017-04-21 14:01:38 -04:00
Axel Kohlmeyer f0681f7e12 add support for USER-TALLY to pair styles hybrid and hybrid/overlay 2017-04-20 14:42:01 -04:00
Axel Kohlmeyer 8d390100e0 update .gitignore and Purge.list for recent changes 2017-04-18 11:44:23 -04:00
Axel Kohlmeyer dee3536144 update VMD molfile plugin headers and move them to lib/molfile (where they belong) 2017-04-18 11:42:31 -04:00
Axel Kohlmeyer 73c210b665 Merge branch 'unstable' of https://github.com/ketankhare/lammps into small-fixes-and-updates 2017-04-18 11:20:23 -04:00
Axel Kohlmeyer 4bad52f30c fix typos 2017-04-17 17:52:06 -04:00
Axel Kohlmeyer 481927ff16 correct 'thrid' instead of 'third' 2017-04-17 17:49:49 -04:00
Axel Kohlmeyer 6c2dd7ebb1 pass the name of the python interpreter compatible with the python package to 'make install-python' 2017-04-14 11:44:36 -04:00
Axel Kohlmeyer d3187b22c4 restore lost change to PYTHON/Install.sh 2017-04-13 18:11:57 -04:00
Steve Plimpton 2f32fb7f8b patch 13Apr17 2017-04-13 11:19:48 -06:00
Richard Berger e6f30ebc9c Merge remote-tracking branch 'origin/master' into python_refactoring 2017-04-12 20:26:57 -04:00
Richard Berger 961096f9df Prevent segfault if Python was never initialized 2017-04-12 11:17:15 -04:00
Richard Berger 3fa9f0a27b Delete python_wrapper.h 2017-04-11 21:51:21 -04:00
Richard Berger 05d7bc556f Initialize Python interpreter in PythonImpl constructor 2017-04-11 21:46:33 -04:00
Richard Berger 2d8bce78a6 Refactor PYTHON package and wrapper classes 2017-04-11 21:22:30 -04:00
Richard Berger 9a027a01da Add Python 3 compatibility to PYTHON package 2017-04-11 20:24:42 -04:00
Steve Plimpton 4da8c1c4e2 patch 11Apr17 2017-04-11 09:00:37 -06:00
Steve Plimpton 49dd9449b8 fix gcmc updates from Aidan, trimming of output for replica commands 2017-04-11 08:35:09 -06:00
sjplimp 76fd936972 Merge pull request #443 from Pakketeretet2/user-manifold-fix-every-keyword 
User manifold fix every keyword
 2017-04-11 08:27:53 -06:00
sjplimp 06cebb9fb4 Merge pull request #445 from Pakketeretet2/extract_for_bond 
Extract for bond
 2017-04-11 08:27:31 -06:00