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1430 Commits

Author SHA1 Message Date
Christoph Junghans e601fa4e8d cmake: add example CMakeLists.txt for xamples/COUPLE/simple 2020-03-26 08:42:00 -06:00
iafoss 9c51bb6cb3
Merge pull request #4 from lammps/master 
update
 2020-03-25 21:25:33 -04:00
iafoss fa4ef70829 code issues 2020-03-25 20:18:07 -04:00
iafoss a8fc2005d4
Merge branch 'master' into feature-cnt 2020-03-20 14:35:57 -04:00
iafoss 53ccc4c607 fix code related issues 2020-03-20 14:21:24 -04:00
Steve Plimpton 8b0e5c66ea tweak the docs for the new fix numdiff command 2020-03-20 07:23:01 -06:00
Axel Kohlmeyer 17dd794514
Merge pull request #1891 from charlessievers/fix_numerical_differentiation 
New fix to compute properties by numerical differences
 2020-03-18 23:31:18 -04:00
Axel Kohlmeyer 164bf1b60e
Merge pull request #1883 from evoyiatzis/master 
Coulomb pair style with smeared out charges (coul/slater)
 2020-03-18 20:52:47 -04:00
Eisuke Kawashima ca1e1e2dff
Convert British spelling to American 2020-03-18 23:09:23 +09:00
Eisuke Kawashima 649a8cc01a
Fix typo 2020-03-14 13:57:48 +09:00
Eisuke Kawashima 8af9d40392
Update DOI resolver 
https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
 2020-03-12 16:53:24 +09:00
Sievers a1188c035b Merge branch 'master' of https://github.com/charlessievers/lammps into fix_numerical_differentiation 2020-03-10 16:14:20 -06:00
Sievers 903e33d86e Added atom map into example, enforce atom map added to fix_numdiff, added error statement to fix_numdiff.h 2020-03-09 10:33:04 -06:00
Axel Kohlmeyer a6086c279b
rename USER-MESO package to USER-MESODPD and update related files and folders 2020-03-09 09:48:49 -04:00
iafoss bdbbe00ec7 Merge branch 'master' into feature-cnt 2020-03-06 18:41:38 -05:00
Jacob Gissinger 21f2ec3a25
Merge branch 'master' into bond/react-new-examples-and-package 2020-03-05 20:08:19 -07:00
Sievers 36ec95c2f5 fixed typo in numdiff example input 2020-03-05 09:55:25 -07:00
Sievers be138d368e Merge branch 'master' into fix_numerical_differentiation 2020-03-04 19:11:39 -07:00
Sievers 968f44601c Updated doc page with delta info and simplified example 2020-03-04 19:08:57 -07:00
julient31 a739b8c6b7 Commit JT 030320 
- modified fix/precession for correct mag energy calc.
- reran all benchmark / examples in serial for verif
- to do: rerun mpi examples, and clean code
 2020-03-03 07:32:13 -07:00
Steve Plimpton 0723bf3db7 setup issues with fix numdiff 2020-03-02 13:32:05 -07:00
Axel Kohlmeyer 6e7e365981
Merge pull request #1888 from lammps/release-preparation 
Documentation and Build script and Info updates for stable release
 2020-02-27 13:23:08 -05:00
Evangelos Voyiatzis d89db2ac2a
files generated by the in.slater example script 2020-02-27 16:03:07 +01:00
Evangelos Voyiatzis 7849de15b0
Create in.slater 2020-02-27 16:01:38 +01:00
Axel Kohlmeyer 275626a1de
re-enable perpertual neighborlist for compute entropy/atom if avg flag is used only 2020-02-26 13:57:11 -05:00
Sievers 13bff07606 Added documentation, added an example, avoided position round off, added in compute_pe's compute_scalar, now fix produces per-atom array instead of global array 2020-02-25 15:32:37 -07:00
Axel Kohlmeyer e87b3a21c2
complete documentation for LAMMPS plugin coupling example 2020-02-25 14:10:55 -05:00
Axel Kohlmeyer 4180b4a7d6
add example to COUPLE folder demonstrating loading LAMMPS as a plugin. 2020-02-25 19:07:49 +01:00
Axel Kohlmeyer 02e287bf51
convert pair styles dpd to exp6 2020-02-24 15:41:16 -05:00
jrgissing ec887b37da Merge branch 'master' of https://github.com/lammps/lammps into bond/react-new-examples-and-package 2020-02-17 21:34:20 -07:00
Axel Kohlmeyer 4cacc4701d
update plumed support to include version 2.6.0. Fix bug in API check 2020-02-13 16:03:58 +01:00
iafoss 0204bf286b CNT package 
The tubular potential model (TPM) force field for Carbon Nanotubes (CNTs) package.
 2020-02-06 16:50:38 -05:00
Axel Kohlmeyer 21a80e9b50
fix typo 2020-01-31 15:57:52 -05:00
Axel Kohlmeyer 8fd2ab78f1
Merge branch 'master' into nwchem 
# Conflicts:
#	doc/src/Howto_client_server.rst
#	doc/src/server_md.txt
 2020-01-31 15:56:25 -05:00
jboschen bc3807aa4b Fix sign of forces in AO mode, update h2o examples 2020-01-31 00:42:00 -06:00
Axel Kohlmeyer f872d374a0
Merge branch 'adaptglok' of github.com:jguenole/lammps into adaptglok 2020-01-30 17:00:10 -05:00
Julien Guénolé 60b9627657 one missing example 2020-01-29 17:48:58 +01:00
Axel Kohlmeyer c855bbb6bf
Merge branch 'master' into adaptglok 2020-01-29 11:42:25 -05:00
Julien Guénolé 6bd23f4909 New example folder for fire 2020-01-29 17:31:20 +01:00
Axel Kohlmeyer 795a872bf3
Merge pull request #1847 from pdebuyl/fix-active 
Add fix propel/self
 2020-01-20 16:57:04 -05:00
Podhorszki Norbert 41cfb91d7d Reformat README and mention about the timeout option 2020-01-20 15:55:31 -05:00
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
Podhorszki Norbert 95d3b9e708 Change BPFile to BP4 in adios config so that streaming through files is enabled 2020-01-20 14:35:51 -05:00
Pierre de Buyl 8ed271f16f change mode of propel/self to quat instead of quaternion 2020-01-20 17:41:20 +01:00
Podhorszki Norbert 50062d6a44 Added rerun example for ADIOS dump/read_dump to examples/USER/adios/rerun. 
Moved the balance example under examples/USER/adios/balance
 2020-01-20 11:23:18 -05:00
Podhorszki Norbert fdd330256c update adios example input file to show more read_dump options 2020-01-20 09:23:35 -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
Pierre de Buyl af1e797271 fix mass and nve/asphere 
1. Set mass to 1. The radius is 1/2, so the density must be
   1/(4/3 pi 1/2^3)
2. Use nve/asphere instead of nve. Else, the particle's orientation are
   not integrated.
 2020-01-20 12:48:26 +01:00
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 d739e017ad
tweak examples to be shorter/faster 2020-01-19 12:22:22 -05:00
Pierre de Buyl 4c8a857960 Merge branch 'master' into fix-active-rebase-5 2020-01-17 22:11:55 +01:00
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
Philipp Kloza cb20d73a82 consistent name for pot file, symbolic link in examples 2020-01-15 20:45:13 +00:00
Axel Kohlmeyer 48cdd6c2fb
refactor mesocnt example to be better suited for testing and add logs 2020-01-15 14:23:19 -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 331fff0613 moved files to USER-MISC, added README entry, added examples 2020-01-15 12:07:26 +00:00
Steve Plimpton ceeae57172 enhanced stochastic wall example 2020-01-14 13:20:35 -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
Steve Plimpton 531946a35f updated hyper examples 2020-01-14 11:14:48 -07:00
To Quy-Dong 00ffa5cc10
Create in.shearflow 2020-01-14 18:58:38 +01:00
Steve Plimpton 99dc283f82 Merge branch 'master' into message-iterate 2020-01-13 09:30:51 -07:00
Axel Kohlmeyer ebdc4b1ce3
rework npt/cauchy example to use bundled potential, run shorter and move to proper folder 2020-01-12 14:46:55 -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 587fc9d962
Merge pull request #1828 from lammps/post-patch-tweaks 
minor omissions in recent patch release
 2020-01-11 21:00:09 -05:00
Axel Kohlmeyer 67b9fd10cc
rename output files to correctly match the used version 2020-01-11 16:12:58 -05:00
Steve Plimpton d5192c1043 added an example for recalculating the RDF at a longer cutoff via rerun 2020-01-10 14:37:45 -07:00
Steve Plimpton 6e3559a6e7 added rerun example dir 2020-01-10 14:09:38 -07:00
Stefan Paquay 60c0270375 Added option to impose fix propel/self only to specific types 2020-01-10 11:32:03 +01:00
Stefan Paquay 6240a7e278 Fixed example 3d_quaternion 2020-01-10 11:32:00 +01:00
Stefan Paquay f7bbc81d9b Added angular momentum thermostatting to 3d quaternion example. 2020-01-10 11:32:00 +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 3d813fec6b Slightly modified example. 2020-01-10 11:31:19 +01:00
Stefan Paquay c93ca5b4a4 Added a fix to add active force to particles. 2020-01-10 11:31:16 +01:00
jrgissing c3922c7e35 rename package USER-REACTION 2020-01-09 20:07:41 -07:00
Steve Plimpton 664227ff11 one more tweak 2020-01-09 17:41:02 -07:00
Steve Plimpton d1222bd3c0 minor omissions in recent patch release 2020-01-09 17:38:50 -07:00
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 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
Dan S. Bolintineanu 7bc8c8e9d8 Minor tweaks to in.rigid.gravity example 2020-01-06 21:26:34 -07:00
Dan S. Bolintineanu 6aa4f4caf6 Added example script and input data file showing benefits of new fix gravity and fix rigid options 2020-01-06 21:18:00 -07:00
jrgissing 1dc8d4acaa bond/react: repackage examples 2020-01-01 12:58:10 -05:00
jrgissing 293e5c3242 bond/react: tiny polystyrene example 2019-12-31 19:35:42 -05:00
jrgissing 895c6be182 bond/react: tiny epoxy example 2019-12-31 19:32:28 -05:00
Vsevak 081839b449 Fix the example according to the convention 2019-12-19 16:44:32 +03:00
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 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