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1295 Commits

Author SHA1 Message Date
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 e68824a392
Merge pull request #1772 from ohenrich/user-cgdna 
USER-CGDNA oxRNA2 Implementation
 2019-12-06 12:23:47 -07:00
Richard Berger e08ba3f11e Merge branch 'master' into library_interface_update 2019-12-03 12:51:17 -05:00
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
Richard Berger 3ce020eab2
Merge pull request #1779 from athomps/compute-snap 
Compute snap
 2019-12-01 12:52:22 -07:00
julient31 8bca0b13f1 Commit2 JT 112219 
- correcting issue in src/SPIN/atom_vec_spin.cpp (inconsistency packing/unpacking hybrid)
- rerunning all examples with corrections of former commit
 2019-11-22 16:29:37 -07:00
julient31 b4ba356f7b Commit JT 111919 
- generated fresh log. files in examples
- corrected some of the examples
 2019-11-19 15:50:56 -07:00
julient31 a0c51b40b9 Commit2 JT 111919 
- renaming validation directory
 2019-11-19 12:54:30 -07:00
julient31 b109fd1687 Commit JT 111919 
- modified named of tests, from benchmark to validation
 2019-11-19 12:50:52 -07:00
Aidan Thompson 921d0794bb Finished documentation and example 2019-11-19 00:12:57 -07:00
Aidan Thompson 59af51ca91 Added code to create pressure compute snap_press behind the scenes 2019-11-18 23:51:08 -07:00
Aidan Thompson 11961084ce Made compute snap fully parallel 2019-11-18 21:35:32 -07:00
Vsevak 7f448a02b1 Add examples/water 2019-11-17 22:01:29 +03:00
Oliver Henrich f4491011d0 Modified README 2019-11-15 18:54:37 +00:00
julient31 0346a3d6d1 Commit JT 111519 
- add README file to the benchmark examples repo
- removed comments from src/SPIN files
 2019-11-15 10:53:39 -07:00
Oliver Henrich f96520ffc6 Added unique base pairing 2019-11-15 17:49:17 +00:00
Oliver Henrich 1df3a71734 Updated documentation 2019-11-15 15:35:19 +00:00
julient31 93bd2f4ab0 Commit JT 111319 
- addind 4 first benchmark examples (in examples/SPIN/benchmark)
- corrected typo in examples (in dump commands)
 2019-11-13 20:46:28 -07:00
Richard Berger 78d5bc3d12 Merge branch 'master' into library_interface_update 2019-11-12 15:17:32 -05:00
julient31 d64bc2a1b7 Commit JT 110419 
- commit changes examples
 2019-11-04 08:05:07 -07:00
Oliver Henrich 84165da4e7 Deleted old log files 2019-10-17 19:34:04 +01:00
Oliver Henrich c6f637f78f Merge branch 'master' into user-cgdna 2019-10-17 18:40:50 +01:00
Oliver Henrich 5652154b3c Added log files 2019-10-17 18:37:55 +01:00
Oliver Henrich b29a962032 Corrected r_stk_high coefficient 2019-10-17 16:16:28 +01:00
Axel Kohlmeyer bfcab685ce
add reference outputs to example input 2019-10-15 17:28:35 +02:00
charlie sievers 9c5c33e869 Updated gjf examples 2019-10-14 14:39:45 -07:00
Steve Plimpton f2840176b3 clarified the README 2019-10-08 18:14:32 -06:00
Steve Plimpton 945f903683 added an examples/UNITS dir 2019-10-08 18:02:21 -06:00
Axel Kohlmeyer 0e10fbb133
Merge pull request #1690 from charlessievers/third_order 
Added third order, added documentation, took out extraneous lines, ad…
 2019-10-08 21:57:15 +02:00
Axel Kohlmeyer 8c063343a1 Merge branch 'master' into collected-small-changes 2019-10-07 18:54:33 +02:00
julient31 ed467d8867 Merge branch 'master' of github.com:alxvov/lammps into OSO 
- solved conflict in doc/src/fix_nve_spin.txt
 2019-10-04 08:56:49 -06:00
Axel Kohlmeyer ed5678d646
Merge pull request #1673 from charlessievers/lammps_gjf 
Lammps fix langevin updates for gjf option
 2019-10-04 10:02:46 +02:00
Steve Plimpton b9d68f93af remove debug statement 2019-10-03 17:04:40 -06:00
Steve Plimpton 5c92e5aa01 added W minimization example 2019-10-03 17:02:04 -06:00
jboschen 319df973d9 Fix typo in cmd line 2019-10-02 11:27:21 -05:00
jboschen 80168d0d5a Automatically append input file to nwchemcmd 2019-10-02 11:11:50 -05:00
Steve Plimpton 214850088b add NWChem wrapper to client/server mode for AIMD 2019-09-27 15:28:48 -06:00
charlie sievers 8c4798b692 added dynamical matrix python script 2019-09-26 12:39:55 -07:00
Axel Kohlmeyer 5d88e12583
correct model comment and remove trailing whitespace 2019-09-25 14:33:07 -04:00
julient31 a0974bc09d Commit JT 092419 
- changed the nve/spin lattice option
- from (yes/no) to (moving/frozen)
- changed the doc and all examples
 2019-09-24 15:58:22 -06:00
julient31 a31aa5debc Merge branch 'master' of github.com:alxvov/lammps into OSO 2019-09-23 14:22:26 -06:00
julient31 bc0ff0db61 Commit2 JT 092319 
- added enum to min.h (for norm choice)
- completed doc min_modify
- corrected torque tol issue in spin/min
 2019-09-23 13:48:33 -06:00
Axel Kohlmeyer d84cbe49a4
Merge pull request #1686 from cusentino/snap-WBe-example 
Added W-Be example to example/snap folder
 2019-09-19 15:38:35 -04:00
Axel Kohlmeyer 3fd43224b3
update comments in example inputs 2019-09-19 15:17:52 -04:00
Axel Kohlmeyer 415698d570
update examples/README 2019-09-19 13:53:54 -04:00
Axel Kohlmeyer ed6dd1a632
Merge pull request #1666 from tanmoy7989/local_density 
added LD potential and wrote html-style doc
 2019-09-19 11:45:46 -04:00
Mary Alice Cusentino e847777e43 Added W-Be example to example/snap folder 2019-09-18 14:34:20 -06:00
charlie sievers eba10b10e8 Merge remote-tracking branch 'origin/master' into lammps_gjf 2019-09-17 12:08:12 -07:00
Axel Kohlmeyer d4d5f241eb
use improper style fourier instead of non-existing style opls 2019-09-17 14:48:58 -04:00
Aidan Thompson 790d7d9fae Added log files and updated README 2019-09-13 15:59:25 -06:00
charlie sievers a948a34f8a added false positive, removed graphs from examples, updated langevin kokkos, improved diff readability in langevin 2019-09-12 16:34:15 -07:00
Richard Berger 34dbcf4f20 Update example 2019-09-12 13:53:29 -04:00
Richard Berger 69854eab42 Expose Neighbor lists via library interface 2019-09-12 13:46:05 -04:00
charlie sievers 7aab3797b3 Updated MD results readme 2019-09-10 17:14:44 -07:00
charlie sievers 90296b76e3 Added a readme to the md results folder 2019-09-10 17:11:49 -07:00
charlie sievers e34b7840d5 Updated documentation and added MD results 2019-09-10 15:53:32 -07:00
charlie sievers f0b6ca82dd Merge branch 'master' into lammps_gjf 2019-09-10 15:39:28 -07:00
charlie sievers 00ee32b582 Merge remote-tracking branch 'upstream/master' 2019-09-10 15:33:04 -07:00
tanmoy.7989 8c113f5fdb added LD potential and wrote html-style doc 2019-09-09 01:51:04 -07:00
Aidan Thompson fb702fa9d6 Added FCC, BCC, and ICOS examples 2019-08-25 23:02:41 -06:00
Aidan Thompson aa9b805cc9 started on W_l 2019-08-23 18:11:52 -06:00
julient31 8ec4e3fc91 Commit JT 082219 
- modified min spin names (removed oso from spin/cg and spin/lbfgs)
- modified associated option name (from spin_oso_cg to spin/cg, same for
lbfgs)
- modified .gitignore, doc pages, and examples accordingly
 2019-08-22 10:48:58 -06:00
Axel Kohlmeyer bf85bff783
Merge pull request #1641 from rbberger/fix_external_via_python 
Extend lib interface to allow setting fix external callbacks
 2019-08-21 10:54:59 -04:00
alxvov 12c73e7a61 Merge branch 'upstream-master' into OSO 2019-08-21 14:03:42 +00:00
Axel Kohlmeyer 6b1df07298
compute HMA style name should be lowercase 2019-08-20 19:24:22 -04:00
Richard Berger 9b703c6675 Fix file name 2019-08-20 16:54:37 -06:00
Richard Berger 2b42428d28 Extend lib interface to set fix external callback 
This allows creating a callback in Python and attaching it to
a fix external instance.
 2019-08-20 14:04:49 -06:00
Stan Moore 9a849a4d4f
Merge branch 'master' into master 2019-08-19 15:55:39 -06:00
charlie sievers ef3f382f61 fixed tbias 2019-08-07 17:27:35 -07:00
Ryan S. Elliott 8619462b3b Added logs for examples/kim 2019-08-07 16:14:22 -05:00
charlie sievers 131d5f0e69 Merge branch 'master' into lammps_gjf 2019-08-07 12:09:22 -07:00
charlie sievers f0f909996a Merge remote-tracking branch 'upstream/master' 2019-08-07 12:03:33 -07:00
Axel Kohlmeyer 5fd323fe32
simplify example folder for ilp/graphene/hbn potential 
- flatten directory structure
- remove CPU time and reduce excess precision from output
- delete redundant and unused files
- regenerate reference outputs
 2019-08-01 14:24:47 -04:00
Axel Kohlmeyer fa6a990536
reduce output precision to default and don't output per-step cpu time 2019-08-01 13:31:52 -04:00
oywg11 76bac4cedc Fix communication bug of ILP 2019-08-01 16:39:42 +03:00
oywg11 8f5cd8661f Fix communication bug of ILP 2019-08-01 16:38:19 +03:00
Stan Moore 602b4a47c0 Fix failing regression test 2019-07-30 10:37:27 -06:00
julient31 b5621b2c90 Merge branch 'master' of github.com:alxvov/lammps into OSO 
Conflicts:
	src/SPIN/neb_spin.cpp
 2019-07-30 09:14:49 -06:00
Axel Kohlmeyer 8fa4efa08e
Merge pull request #1440 from ellio167/kim-simulator-models 
Develop native support for KIM simulator models
 2019-07-30 10:53:58 -04:00
alxvov 9609c75073 Use descent condition, and no line search as a default option for 
all oso
 2019-07-30 11:16:40 +00:00
Axel Kohlmeyer 88523fdd6e
Merge pull request #1529 from rupertnash/compute_momentum 
add compute momentum command
 2019-07-29 22:51:29 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 7043b9f620
Merge pull request #1548 from jrgissing/bond/react-clarify-how-stabilization-works 
Bond/react clarify how stabilization works
 2019-07-29 19:55:24 -04:00
Ryan S. Elliott 0f059c56f9 Add details about installing models to KIM example input 2019-07-29 15:30:46 -05:00
casievers cc96ea1ded added respa compatability, and simplified examples 2019-07-25 15:23:01 -07:00
Ryan S. Elliott fadb40051b Update kim_query & clear and update examples/kim 2019-07-25 14:03:35 -05:00
casievers 13f4fe186b Updated examples/gjf/README.md 2019-07-24 16:30:02 -07:00
casievers b97e856bf2 Tally works and example readmes addes 2019-07-24 16:21:49 -07:00
casievers f4da632870 recent change to gjf tally (not working) 2019-07-24 16:21:49 -07:00
casievers e38072f365 added lammps python example 2019-07-24 16:21:49 -07:00
casievers 4a80edd75f updated fix_langevin and made example 2019-07-24 16:21:48 -07:00
alxvov f9ed12be4f modify line for spin_cubic, spin_none. edit docs a bit. 2019-07-24 23:21:07 +00:00
julient31 f1c3b9d0bf Commit2 JT 072319 
- corrected some mistakes in doc files
- modified oso examples to match new line options
 2019-07-23 11:24:52 -06:00
julient31 f0679cff6d Commit JT 072319 
- added 2 oso examples in examples/SPIN/spinmin
- added doc for oso_cg and oso_lbfgs
 2019-07-23 09:27:15 -06:00
Rupert Nash 243ce8dbfc
Merge branch 'master' into compute_momentum 2019-07-22 09:48:08 +01:00
Ryan S. Elliott 03d26f6f6f Merge branch 'master' into kim-simulator-models 2019-07-21 13:59:48 -05:00
Oliver Henrich c2643a519e Clarified explanation of new example3 2019-07-19 13:29:39 +01:00
Oliver Henrich 57fd9723a5 Added comment on new duplex3 2019-07-19 12:30:01 +01:00
Oliver Henrich 7bf9757755 Updated input and log files, amended comment in data files 2019-07-19 11:57:58 +01:00
Ryan S. Elliott 1f47da6c51 Add fixed_types to kim_init & split to kim_query 2019-07-08 17:46:47 -05:00