jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
13,809 Commits 9 Branches 198 Tags 1.1 GiB
Commit Graph

13809 Commits

Author SHA1 Message Date
Rodolfo Leite 941ee565a1 Added lal_ufm_ext.cpp in lib/gpu 2017-10-24 11:12:51 -02:00
Rodolfo Leite b63acf6843 Added the UFM files (doc/src - lib/gpu - src) 2017-10-24 11:11:10 -02:00
Steve Plimpton a7ad12491f Merge pull request #706 from lammps/doc-cs 
update to doc pages for new coreshell pair styles
 2017-10-21 16:12:23 -06:00
Steve Plimpton 2137be3219 update to doc pages for new coreshell pair styles 2017-10-21 15:50:27 -06:00
Steve Plimpton ce78f6943d Merge pull request #705 from akohlmey/fix_rigid_bugfix 
fix segfault bug in fix rigid/small found by regression testing
 2017-10-20 17:01:50 -06:00
Steve Plimpton 998aedc6c1 Merge pull request #670 from vishalkenchan/pair_style/coul_wolf_cs 
add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package
 2017-10-20 16:09:33 -06:00
Axel Kohlmeyer 0a02c3c78c fix segfault bug for in fix rigid/small found by regression testing 2017-10-20 16:56:06 -04:00
Steve Plimpton aaf5e87c84 Merge pull request #703 from akohlmey/custom-rigid-body-generation 
Allow rigid body generation from custom properties
 2017-10-20 14:08:15 -06:00
Steve Plimpton 2d0f5e277c Merge pull request #704 from akohlmey/bond-gromos-bugfix 
Compute energy correctly for bond style gromos
 2017-10-20 14:06:35 -06:00
Steve Plimpton 260bbc6f9f Merge pull request #702 from giacomofiorin/colvars-fix-the-fix 
Fix a Colvars error that was hidden by the previous segfault
 2017-10-20 14:06:15 -06:00
Axel Kohlmeyer 6b34a30528 compute energy correctly for bond style gromos 2017-10-20 14:53:22 -04:00
Axel Kohlmeyer 83c7d3a1d2 update fix rigid documentation 2017-10-20 14:18:50 -04:00
Axel Kohlmeyer 961b976374 add/correct code to define rigid bodies with atomstyle/atomfile variables and via custom per-atom properties 2017-10-20 13:56:09 -04:00
Axel Kohlmeyer ac6434e496 add input examples for custom rigid body definition 2017-10-20 13:54:45 -04:00
Giacomo Fiorin f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
vishalkenchan e284545c5b added some documentation and reference example 2017-10-20 12:03:22 +02:00
Steve Plimpton e368acdaeb Merge pull request #700 from giacomofiorin/colvars-fix 
Import segfault fix in Colvars module
 2017-10-19 11:45:36 -06:00
Giacomo Fiorin 6e7504f153 Import segfault fix in Colvars module 2017-10-19 08:09:44 -04:00
vishalkenchan 71c4edda51 add coul/wolf/cs and born/coul/wolf/cs pair styles for CORESHELL package 2017-10-19 13:21:13 +02:00
Steve Plimpton 40147a7a64 Merge pull request #699 from lammps/doc-update2 
cross ref fix deform and new fix nvt/uef in doc pages
 2017-10-18 16:44:18 -06:00
Steve Plimpton f709a723cd cross ref fix deform and new fix nvt/uef 2017-10-18 15:26:15 -06:00
Steve Plimpton 6dd55e49cb Merge pull request #698 from lammps/doc-update 
small updates to recently added docs and rename of an example dir
 2017-10-18 15:24:54 -06:00
Steve Plimpton 281b1dc375 small updates to recently added docs and rename of an example dir 2017-10-18 14:56:47 -06:00
Steve Plimpton e93f8f8889 Merge pull request #671 from danicholson/user-uef 
USER-UEF package for extensional flow
 2017-10-18 13:38:56 -06:00
Steve Plimpton 35f2cfa0bf Merge pull request #669 from urpedersen/master 
fix rhok - biasing long-range order
 2017-10-18 13:31:15 -06:00
Steve Plimpton e44196c011 Merge pull request #694 from akohlmey/bond-gromos 
Add gromos bond style
 2017-10-18 13:27:15 -06:00
Steve Plimpton 2fe1d1b904 Merge pull request #697 from andeplane/fix_heat_bug 
Avoid checking region when not specified
 2017-10-18 13:26:19 -06:00
Steve Plimpton b1b4a52b14 Merge pull request #695 from timattox/USER-DPD_small_updates 
USER-DPD small updates
 2017-10-18 13:25:48 -06:00
Steve Plimpton 382de50341 Merge pull request #696 from wmbrownIntel/intel-update-oct17 
Bug fix for unexpected case where a Intel bonded style is specified but there are no types
 2017-10-18 13:25:07 -06:00
Steve Plimpton 7dfc6b7eab Merge pull request #688 from lammps/history 
refactoring of neighbor history
 2017-10-18 13:24:36 -06:00
Anders Hafreager 19eb5d3897 Avoid checking region when not specified 2017-10-18 18:05:34 +02:00
Axel Kohlmeyer 17c17ac409 update multi-threaded neighbor list build for neighbor list refactor 2017-10-18 11:25:15 -04:00
Axel Kohlmeyer 39ededd46c update respa/omp integrator style for neighbor list refactor 2017-10-18 11:24:44 -04:00
Axel Kohlmeyer 2c7528811d update several pair styles to be compliant with refactored respa lists data structures 2017-10-18 11:24:12 -04:00
Steve Plimpton 0966e14e73 more changes to rRESPA neighbor lists 2017-10-17 17:33:01 -06:00
Michael Brown bb141aaae0 USER-INTEL: Bug fix for case where a bond/angle/dihedral/improper style is specified, but there are no bond/... types and therefore no allocation. 2017-10-16 22:51:56 -07:00
Axel Kohlmeyer 374d619769 add gromos bond style 2017-10-16 14:57:12 -04:00
Axel Kohlmeyer 59de1a71c8 Merge branch 'history' of github.com:lammps/lammps into history 2017-10-16 14:37:30 -04:00
Tim Mattox 4c6779cb0d USER-DPD Kokkos: propagate the new neigh_modify options from efaa4c67 
Propogate the efaa4c67 changes to npair_ssa_kokkos from npair_kokkos that
support the new neigh_modify exclude molecule/intra and /inter options.
Note: npair_ssa_kokkos could inherit from npair_kokkos to avoid this kind
of missed change. Unfortunately, inheritance from templated classes is
both tricky and messy, and not worth the complexity in this case, IMHO.
 2017-10-16 13:37:27 -05:00
Axel Kohlmeyer 5fb5f70ec6 update USER-OMP code for shear history neighbor refactoring 2017-10-16 14:37:20 -04:00
Tim Mattox b0bba1976b USER-DPD: remove unused coord2bin() variants, and add ISFINITE checks 2017-10-16 13:36:44 -05:00
Steve Plimpton f8f13d929f Merge pull request #693 from giacomofiorin/colvars-update 
Update Colvars to version 2017-10-11
 2017-10-13 17:25:06 -06:00
Giacomo Fiorin 3e89b270fd Update Colvars to version 2017-10-11 
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
 2017-10-13 13:45:10 -04:00
Stan Moore f6ddc8c7c9 Fix compile errors from neigh history refactor 2017-10-13 10:49:31 -06:00
Steve Plimpton a973c65d67 Merge pull request #691 from akohlmey/collected-fixes 
Collected small changes for next patch
 2017-10-13 09:50:03 -06:00
Steve Plimpton 1a200588bd Merge pull request #689 from rbberger/pylammps_autocomplete_fix 
Limit IPython autocomplete to known commands and properties
 2017-10-13 09:49:03 -06:00
Steve Plimpton 18ca2292c2 Merge pull request #686 from giacomofiorin/lepton-library 
Add Lepton library within lib/colvars
 2017-10-13 09:48:42 -06:00
Steve Plimpton d3ef4bd594 Merge pull request #685 from ellio167/kim-api-v1.9.2 
Update lib/kim for kim-api-v1.9.2
 2017-10-13 09:48:16 -06:00
Axel Kohlmeyer 3df9caf435 drop const qualifier to allow bracketing of lookup index 2017-10-13 10:29:49 -04:00
Axel Kohlmeyer fa2e5ac2d9 handle lookup exceptions consistently across energy and energy+force lookup in bond/angle style table 2017-10-13 10:13:34 -04:00