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12711 Commits

Author SHA1 Message Date
sjplimp 5c0c8bb4cd Merge pull request #558 from lammps/intel 
memory allocation bugfix for USER-INTEL pppm from M Brown
 2017-07-03 12:25:12 -06:00
sjplimp 9eeb97b039 Merge pull request #544 from akohlmey/tip4p-triclinic 
Correct handling of triclinic box support in pppm/tip4p and pppm/tip4p/omp
 2017-07-03 12:24:18 -06:00
Axel Kohlmeyer 9ca9b5e2ff add authors tag to pull request template 2017-07-03 12:06:36 -04:00
Axel Kohlmeyer db73eca29f correct example inputs for recent changes to create_bonds command 2017-07-03 11:43:55 -04:00
Axel Kohlmeyer 2d1941ed9b make USER-INTEL compilable again with gcc and without OpenMP active 2017-07-03 11:33:08 -04:00
Steve Plimpton e634c5a2de memory allocation bugfix for USER-INTEL pppm from M Brown 2017-07-03 08:53:53 -06:00
Axel Kohlmeyer 22f3db4723 remove some dead code and prune argument lists accordingly 2017-07-01 18:16:36 -04:00
Axel Kohlmeyer a1574fc03d remove unused variables 2017-07-01 17:55:13 -04:00
Axel Kohlmeyer d68fb1cbb8 avoid repeated computation of deltaik and deltajk, calls to pow() 2017-07-01 17:49:14 -04:00
Axel Kohlmeyer 060e32973e another speedup by folding dsij() into meam_force() 2017-07-01 17:07:56 -04:00
Axel Kohlmeyer a4a15f24bd fold screen() function into getscreen() and avoid some repeated operations 2017-06-30 18:44:51 -04:00
sjplimp 883b7aaa0e Merge pull request #557 from lammps/create-bonds 
add single options to create_bonds command
 2017-06-30 14:18:15 -06:00
Axel Kohlmeyer 1fff30af90 update or create example outputs for meam and meam/c 2017-06-30 15:30:06 -04:00
Axel Kohlmeyer a490e04d24 add backward compatibility item to pull request template 2017-06-30 15:07:43 -04:00
Axel Kohlmeyer b445f8eadf spell-check new additions to create_bonds doc page 2017-06-30 14:59:08 -04:00
sjplimp b79044d4f6 Merge pull request #554 from jewettaij/master 
Have extra/XXX/per/atom set by keyword to the read_data command
 2017-06-30 11:47:46 -06:00
Steve Plimpton 711afe5062 add single options to create_bonds command 2017-06-30 11:30:43 -06:00
sjplimp 3bf2c60276 Merge pull request #553 from Pakketeretet2/USER-MANIFOLD-gaussian-bump 
Update to USER-MANIFOLD gaussian bump
 2017-06-30 11:08:47 -06:00
sjplimp d5119b2d75 Merge pull request #550 from stanmoore1/kokkos_leakfix 
Fix Memory Leak in Kokkos NeighList
 2017-06-30 11:08:30 -06:00
sjplimp b2b621a2e1 Merge pull request #547 from akohlmey/collected-bugfixes 
Collected small bugfixes and updates
 2017-06-30 11:08:02 -06:00
sjplimp b5250d11f6 Merge pull request #545 from akohlmey/issue-and-pull-request-templates 
Add folder .github containing administrative files for use with GitHub
 2017-06-30 11:06:58 -06:00
Axel Kohlmeyer 9dad95d101 performance improvement through moving inlinable functions to header file 2017-06-30 13:04:09 -04:00
Axel Kohlmeyer f6faad335c update documentation for nb3/harmonic pair style according to e-mail to lammps-users 2017-06-30 11:37:18 -04:00
Sebastian Hütter 5548704700 Move stateless functions to separate module, improve style 
- use static/const
- return instead of ptr-parameter, &ref if more than one return
- replace macros from header with inline functions
- remove useless/old comments
 2017-06-30 15:37:26 +02:00
Sebastian Hütter e0939ac795 Re-Run clang-format 2017-06-30 12:28:22 +02:00
Axel Kohlmeyer d5921e9fb9 consolidate and update error message and read_data documentation for the updated read_data command 2017-06-29 16:30:49 -04:00
Axel Kohlmeyer aa3f4b7690 change the handling of reading "extra XXX per atom", so that the final choice is the larger of the value in the file and the keyword 2017-06-29 16:09:23 -04:00
Andrew Jewett 38075455b6 new keywords for read_data: extra/X/per/atoms + changes to docs 2017-06-28 17:55:30 -07:00
Andrew Jewett fa30635465 Revert "added feature to write_data.cpp to support "extra bonds" (angles,dihedrals,impropers,special)." 
This reverts commit 0c2f7c74be.
 2017-06-28 17:48:32 -07:00
Andrew Jewett 0c2f7c74be added feature to write_data.cpp to support "extra bonds" (angles,dihedrals,impropers,special). 2017-06-28 14:12:03 -07:00
Stefan Paquay 91bce7ccf9 Replaced std::fabs with fabs. 2017-06-28 09:48:00 -04:00
Axel Kohlmeyer d0470799ac consistently check for all per-atom-type masses being set only when per-atom masses are not set 
rather than placing an if statement around every incidence of calling atom->check_mass() to ensure it is only called when per atom masses are not set, we place that check _inside_ Atom::check_mass(). This avoids unexpected error messages.
 2017-06-28 06:26:21 -04:00
Stefan Paquay 076990c28a Updated Gaussian bump so that it has a better taper function. 2017-06-27 16:48:33 -04:00
Axel Kohlmeyer 661e51b607 remove non-ascii characters and spell check 2017-06-27 00:38:53 -04:00
Axel Kohlmeyer d076040471 use itemized list instead of paragraphs for links at the top 2017-06-27 00:24:04 -04:00
Axel Kohlmeyer 2f9c0a3b8e more formatting issues addressed 2017-06-27 00:23:10 -04:00
Axel Kohlmeyer b9d213ee2b update formatting for contributing ToC 2017-06-27 00:21:29 -04:00
Axel Kohlmeyer fa3c7727e1 contributing guidelines, issue and pull request template are now feature complete 
This is still a draft and in need of editing, proofreading and testing for formatting.
 2017-06-27 00:17:37 -04:00
Stan Moore 9fec8a0470 Remove clean_copy function from pair_vashishta_kokkos 2017-06-26 10:56:03 -06:00
Stan Moore b889776557 Fixing memory leak in Kokkos neighborlist 2017-06-26 10:51:26 -06:00
Sebastian Hütter 8fca667e4b Change indexing of remaining variables and locals 
- Voigt index tables
- local variables
- remove shims from header
 2017-06-26 18:09:11 +02:00
Axel Kohlmeyer f7077d9672 Merge branch 'collected-bugfixes' of github.com:akohlmey/lammps into collected-bugfixes 2017-06-26 11:27:31 -04:00
Axel Kohlmeyer f89a7266bf make USER-INTEL compilable again with gcc and without OpenMP active 2017-06-25 23:57:42 -04:00
Stefan Paquay 1257955662 Merge branch 'master' of https://www.github.com/lammps/lammps 2017-06-23 19:31:43 -04:00
Steve Plimpton 1370385c8c patch 23Jun17 2017-06-23 17:10:59 -06:00
sjplimp 2240c3d7d3 Merge pull request #548 from lammps/doc-update 
doc page clarifications for CHARMM energy and dipole pre-factors
 2017-06-23 16:48:37 -06:00
Steve Plimpton 4fcbd58d5a doc page clarifications for CHARMM energy and dipole pre-factors 2017-06-23 15:54:14 -06:00
Axel Kohlmeyer c2c6dc1458 remove spurious comment line 2017-06-23 16:24:37 -04:00
Axel Kohlmeyer 18983c307e fix qeq/reax/omp bugfix from metin 2017-06-23 16:24:00 -04:00
sjplimp 25a5d12af3 Merge pull request #541 from lammps/charmm 
use CHARMM energy conversion factor with new CHARMM pair styles
 2017-06-23 09:10:04 -06:00