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1401 Commits

Author SHA1 Message Date
wverestek 5a9cc9e380 updated log files 2020-04-24 09:35:32 +02:00
wverestek 1751a27ff6 removing example script from nylon melt and adding to tiny nylon 2020-04-22 14:07:11 +02:00
wverestek 0288bb4b6b small modification to fix bond/react to allow equal style variables as probability o 
On branch master
Your branch is up to date with 'origin/master'.

Changes to be committed:
	modified:   doc/src/fix_bond_react.rst
	new file:   examples/USER/reaction/nylon,6-6_melt/in.large_nylon_melt_variable_probability
	modified:   src/USER-REACTION/fix_bond_react.cpp
	modified:   src/USER-REACTION/fix_bond_react.h
 2020-04-22 13:27:10 +02:00
julient31 5eee4cb1ba C4 JT 041420 
- reran all SPIN examples
 2020-04-14 15:44:15 -06:00
Axel Kohlmeyer 41cfb3ae80
Merge branch 'master' into neel-rework 2020-04-14 05:57:08 -04:00
Sievers 9a2348ff15 InP example included 2020-04-09 01:18:34 -07:00
Christoph Junghans bb9ffe2edc simple.c: fix lammps include 2020-04-06 14:15:47 -06:00
Aidan Thompson 47709c4cad Now using mix and match syntax 2020-04-05 00:21:31 -06:00
Aidan Thompson 3329caa7f1 First pass at general ML pair style 2020-04-01 18:07:33 -06:00
Christoph Junghans ef0df90b48 Merge branch 'master' into cmake_clean_up 2020-03-31 14:42:28 -06:00
julient31 22aab4406e Commit3 033020 
- re-checked all validation problems, ready for PR
 2020-03-30 09:32:46 -06:00
julient31 961c554ed6 Merge branch 'clean-master2' of github.com:julient31/lammps into neel-rework 2020-03-30 09:01:30 -06:00
julient31 547d29d030 Commit2 JT 300320 
- regenerated all spin examples
 2020-03-30 08:55:54 -06:00
julient31 51e3f9dcda Commit JT 033020 
- modified all spin pairs (match nve)
- correct doc min_modify
- correct code max norm (square values)
- added draft nvt validation
 2020-03-30 08:09:11 -06:00
Christoph Junghans f30116311f cmake: add simpleC to CMakeLists.txt 2020-03-28 17:57:53 -06:00
Christoph Junghans 4aadb554a3 cmake: replace incl. dir hack by even better hack 2020-03-28 08:43:13 -06:00
Christoph Junghans b245872bae cmake: replace include dir hack by a different hack 2020-03-28 08:28:41 -06:00
Axel Kohlmeyer 5a88db838d
Merge pull request #1946 from yafshar/kim-property 
Add new kim_property command
 2020-03-27 20:58:52 -04:00
Yaser Afshar 24ed8749d2 a kim-property command example 2020-03-27 17:17:04 -05:00
Christoph Junghans 16ac65e8cf cmake: make mpi public again 2020-03-27 15:01:51 -06:00
Christoph Junghans 6f8915e0a5 cmake: updated COUPLE/simple cmake 2020-03-27 13:55:34 -06:00
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