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988 Commits

Author SHA1 Message Date
Rene Halver a90e019ec7 updated ScaFaCoS examples, added open-boundary Hammersley distributed sphere and charged cloud near a charged wall examples 2018-07-23 16:13:15 -06:00
Steven J. Plimpton 2f55981224 new MESSAGE package for client/server/coupling 2018-07-23 15:58:33 -06:00
Steve Plimpton 5c21d2aff9
Merge pull request #962 from ndtrung81/body-dem 
Discrete element models for the BODY package
 2018-07-20 14:37:41 -06:00
Rene Halver 5c934cdb6f fixed examples to work with charged molecular restriction and new kspace call format 2018-07-20 10:40:29 -06:00
Steven J. Plimpton b0c9fde1dd more changes from Steve 2018-07-18 15:32:03 -06:00
Steven J. Plimpton 843b96e8dd more changes to new polygon/hedron docs and command names 2018-07-18 08:49:42 -06:00
Steven J. Plimpton d4385ade15 more changes to ATM source and doc file 2018-07-16 11:22:22 -06:00
Steven J. Plimpton e7f4e059cf convert to KSspace style rather than fix 2018-07-13 16:46:06 -06:00
Sergey Lishchuk b461967e91 Updated documentation and source 2018-07-13 20:45:06 +01:00
Sergey Lishchuk bf5fbc92df Updated documentation and source 2018-07-13 20:18:53 +01:00
Rene Halver cdf091f228 fixed an error in the scafacos example (added missing keyword tolerance) 2018-07-13 08:37:29 -06:00
Gareth Tribello c442166ded Tidied up example directory for PLUMED 2018-07-12 16:22:40 +01:00
Gareth Tribello 6d9face1ec Added documentation describing PLUMED package installation 2018-07-12 12:26:09 +01:00
Gareth Tribello 4d5635a3c4 Fixed virial contribution from PLUMED 2018-07-10 16:01:45 +01:00
julient31 9d5dc561ca Commit1 JT 070918 
- created README in examples/SPIN
- modified doc/src/set.txt to define 'spin' and 'spin/random' keywords
 2018-07-10 09:44:14 -04:00
Steven J. Plimpton 13338bf8cb small changes to Trung body files 2018-07-09 16:15:15 -06:00
Steven J. Plimpton 3a824b3a4b mods to Sergey's files 2018-07-09 14:16:46 -06:00
Rene Halver f698e37bf2 merged latest version of CMakeLists.txt with custom one (adding USER-SCAFACOS) 2018-07-09 13:41:35 -06:00
Rene Halver 400ae72267 added tolerance to the example 2018-07-09 13:18:28 -06:00
Rene Halver b259de95d2 fix for ScaFaCoS library 2018-07-09 13:00:52 -06:00
Sergey Lishchuk 7260bb58e1 Added Axilrod-Teller manybody potential 2018-07-04 11:03:30 +01:00
Gareth Tribello 7f5a83cb1d Added first go at checks on PLUMED interface to LAMMPS 2018-07-02 17:04:19 +01:00
Gareth Tribello b299bfa821 Started adding tests on PLUMED interface 2018-07-02 13:58:38 +01:00
Gareth Tribello 2c5f2a6683 Added running example of PLUMED + LAMMPS 
Not sure if this has been done correctly.  I add both the input and the output
 2018-07-02 10:22:23 +01:00
Gareth Tribello 9b44529591 Added an example 2018-06-29 17:46:51 +01:00
Steve Plimpton 6bd5a3d69b
Merge pull request #935 from julient31/spin_origin 
Spin origin
 2018-06-27 16:58:27 -06:00
Steve Plimpton 8e77be0848
Merge pull request #967 from lammps/latte-tweak2 
small changes to last LATTE PR, including xControl to upper case
 2018-06-27 16:44:25 -06:00
Axel Kohlmeyer d3b83885d1 make SPIN package examples consistent with other examples and add reference logs 2018-06-27 14:06:56 -04:00
Axel Kohlmeyer 244963aa19 fix incorrect scaling of emag bug 2018-06-27 12:29:34 -04:00
Axel Kohlmeyer 6008cee6aa ...and replace with symbolic links 2018-06-26 16:02:56 -04:00
Axel Kohlmeyer f33a2c982c remove redundant potential files 2018-06-26 16:01:54 -04:00
Steve Plimpton 8e14143908
Merge pull request #925 from PabloPiaggi/pair_entropy 
Pair entropy fingerprint
 2018-06-26 13:16:09 -06:00
PabloPiaggi f36e1a2cdc Changed default deltabin from 2 to 3 2018-06-26 13:06:04 +02:00
Steven J. Plimpton 49a91db0b2 small changes to last LATTE PR, including xControl to upper case 2018-06-25 17:43:31 -06:00
Steve Plimpton 5e48565761
Merge pull request #961 from cnegre/newsystem 
Added newsystem flag to be passed to latte
 2018-06-25 17:20:57 -06:00
julient31 06b3209ad8 Commit JT 062518 2018-06-25 09:56:39 -06:00
PabloPiaggi 9108306c11 Shorter entropy/atom example 2018-06-24 00:36:09 +02:00
PabloPiaggi 86519ce213 Rename compute to entropy/atom 2018-06-24 00:25:07 +02:00
Christian F. A. Negre dc132c8bf1 Added newsystem flag to be passed to latte 2018-06-21 15:40:20 -06:00
Steven J. Plimpton cbfb751e92 made latte.in compatible with v1.1.1 and updated log files 2018-06-21 11:10:29 -06:00
Christian F. A. Negre 37b901eadb Added boxrel example and simplified latte.in 2018-06-19 11:12:28 -06:00
Axel Kohlmeyer 4a88f53d22 adjust input files for changed paths 2018-06-18 19:17:25 -04:00
Axel Kohlmeyer b2e6863d93 add reference log file. 2018-06-15 17:01:26 -04:00
Trung Nguyen f5e9b1e021 Added example input for fix wall rounded/polygon 2018-05-29 23:59:58 -05:00
Trung Nguyen 1fbd4fffd4 Updated rounded/polygon example 2018-05-29 23:50:43 -05:00
Trung Nguyen d4cca615fb Refactored pair body rounded/polyhedron so that kernel_force() can be derived for other styles 2018-05-29 23:42:03 -05:00
julient31 6457e5eedb Commit1 JT 052918 modifs files 2018-05-29 14:51:21 -06:00
Trung Nguyen 6438cffa57 Added examples for body rounded/polygon 2018-05-26 13:39:43 -05:00
Trung Nguyen dd3278ea07 Added examples for body rounded/polygon and rounded/polyhedron 2018-05-24 23:54:50 -05:00
julient31 5f0e6d0aa7 Commit JT2 052418 2018-05-24 12:55:39 -06:00
PabloPiaggi e550f5120b Updated docs 2018-05-22 12:44:40 +02:00
julient31 1641f78e3e Merge from lammps master 2018-05-21 16:06:53 -06:00
Axel Kohlmeyer 1f193e02e0 update to c++ style include header syntax 2018-05-21 16:49:00 -04:00
PabloPiaggi 124641dc8a Examples - new local option 2018-05-18 15:13:48 +02:00
julient31 437e854741 Commit JT 051118 before CEA 2018-05-11 15:24:26 -06:00
Steve Plimpton 7fed6c7e4c
Merge pull request #634 from craabreu/master 
Computation of forces/torques on rigid bodies moved to post_force
 2018-05-07 14:39:10 -06:00
Axel Kohlmeyer d203118286 update rigid body reference outputs. add bodyforces early examples 2018-05-07 14:19:50 -04:00
Steve Plimpton a7c9418629
Merge pull request #890 from jrgissing/bond_react_final_touches 
bond/react final touches
 2018-05-07 10:37:47 -06:00
Axel Kohlmeyer 9d9d7cb9ed update example log files 2018-05-06 11:10:40 -04:00
jrgissing 916ed71760 fix bond/react final touches 2018-05-06 00:34:03 -06:00
Axel Kohlmeyer f9f8e2bdbe update USER-BOCS example to match LAMMPS style and include reference logs 2018-05-05 11:43:05 -04:00
Axel Kohlmeyer 735bceb468 Merge branch 'master' into USER-BOCS 2018-05-05 10:21:21 -04:00
Axel Kohlmeyer 81293b0fda changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style 2018-05-05 10:21:11 -04:00
Axel Kohlmeyer c9d41178d8 update logfiles and adjust some example inputs to be consistent 2018-05-03 23:37:01 -04:00
Steve Plimpton eeee2d3026
Merge pull request #803 from jrgissing/fix_bond_react 
Fix bond react
 2018-05-03 14:16:46 -06:00
Axel Kohlmeyer 53cc609c4c make filenames comply with LAMMPS conventions and add reference log files 2018-05-03 16:03:37 -04:00
Axel Kohlmeyer b5b70b429f update log files for SNAP package examples to reflect current state of keywords. 2018-05-03 13:00:24 -04:00
Michael DeLyser ed3f8d4b3f
Update methanol.lmp 2018-05-02 11:28:44 -04:00
julient31 392816a807 Commit JT 042418 
- adding the README
- some corrects pair_spin*.cpp/h
 2018-04-26 15:26:31 -06:00
julient31 1b8669c620 Commit JT 042018, new spin/precession and pair/spin (peru virtual) 2018-04-26 15:26:31 -06:00
julient31 ce80d1a3ea Commit JT 041618 
Enabling multiple exchange interactions
 2018-04-26 15:26:31 -06:00
julient31 8709f6044b Commit modifs before release 2 (04/02/18) 2018-04-26 15:26:31 -06:00
julient31 a315599bac Commit modifs before release 1 (03/26/18) 2018-04-26 15:26:31 -06:00
julient31 08bc115380 Commit before meeting 032218 2018-04-26 15:26:13 -06:00
julient31 65b7e43a91 Examples and docs 2018-04-26 15:25:23 -06:00
julient31 2a3b93ca3d First commits last version doc 2018-04-26 15:21:41 -06:00
julient31 e4c6c46b4c Commit JT 010318 (before APS) 2018-04-26 15:21:41 -06:00
julient31 7990826ca2 Commit JT 021518 2018-04-26 15:21:41 -06:00
julient31 fa499ff95d Commit JT 021318 2018-04-26 15:21:41 -06:00
julient31 86cfbb3010 Delete in.spin.read_data 2018-04-26 15:15:16 -06:00
julient31 f409f4ff53 Commit JT 021318 2018-04-26 15:02:15 -06:00
julient31 eab737a45c Delete Co_PurjaPun_2012.eam.alloy 2018-04-26 15:01:43 -06:00
julient31 b422480002 Commit JT 021318 2018-04-26 15:01:43 -06:00
julient31 3d18f55155 commit JT 020818 
- adding files for doc and reorg.
 2018-04-26 15:01:43 -06:00
julient31 6490ee46b7 Commit JT 020618 
- Documentation
- Memory leaks solved
 2018-04-26 14:58:43 -06:00
julient31 642c8f9859 Commit JT 020518 
Begin work documentation
 2018-04-26 14:58:43 -06:00
julient31 755bda2275 Commit JT 020118 2018-04-26 14:58:43 -06:00
julient31 05a7e5011f Commit JT 012318 2018-04-26 14:58:43 -06:00
julient31 3abb7f0eaf Commit JT 011718 
Correction bug in fix/integration/spin
 2018-04-26 14:58:43 -06:00
julient31 5b93fc6a27 Commit JT 011617 2018-04-26 14:58:43 -06:00
julient31 1e096d77ef Commit JT 011518 2018-04-26 14:58:43 -06:00
araven 38e940a392 beautyfy shell script 2018-04-26 14:58:43 -06:00
araven 7cc62f4234 minor updates on examples/SPIN 2018-04-26 14:58:43 -06:00
araven 01f378d265 minor updates on examples/SPIN 2018-04-26 14:58:43 -06:00
julient31 ab200cff06 - linked list in the integration algorithm 
- new version of the coord2sector function
- possible to read_data a spin .data file
 2018-04-26 14:58:43 -06:00
julient31 5fe0b0a2cc Delete in.cobalt_dev 2018-04-26 14:58:42 -06:00
julient31 6df54ac3ec Delete in.cobalt_SD 2018-04-26 14:58:42 -06:00
julient31 1e9d91bd8f Delete in.co_magnetomech 2018-04-26 14:58:42 -06:00
julient31 749336ae1f Delete in.kagome 2018-04-26 14:58:42 -06:00
julient31 148d26d943 Delete in.cobalt 2018-04-26 14:58:42 -06:00
julient31 2bfd30f7d7 Delete in.BFO 2018-04-26 14:58:42 -06:00
julient31 f4bb33de4b Memory corrections 2018-04-26 14:58:42 -06:00
julient31 49f0a7a89a New MPI algorithm (still to be checked) 2018-04-26 14:58:42 -06:00
julient31 f1182df776 Commit MPI algorithm 2018-04-26 14:58:42 -06:00
araven 1828274a99 new vmd shell to prepare vmd runs 2018-04-26 14:58:42 -06:00
araven 813343928a moving files into proper directories 2018-04-26 14:58:42 -06:00
julient31 f5ff30df83 Changes for coupling magnetomech: 
- hybrid_overlay friend with fix_nve_spin
- modif of the allocation of pair classes in fix_nve_spin
- modif input file for hybrid/overlay eam - spin/pair
- new file for cobalt eam potentials
 2018-04-26 14:58:41 -06:00
julient31 45ea7b3cc7 First version of the spin tutorial (2) 
Examples (example/SPIN), for BFO and Co
 2018-04-26 14:58:41 -06:00
MICHAEL ROBERT DELYSER c5e884fb41 USER-BOCS 2018-04-26 09:34:47 -04:00
Axel Kohlmeyer 4fa95de91c update logfiles for gcmc example inputs 2018-04-04 12:33:48 -04:00
Axel Kohlmeyer 24e0ca5377 avoid warning about group all 2018-04-04 12:28:20 -04:00
Aidan Thompson d1356c1d76 Made ndof dynamic for temperature fixes and computes 2018-04-03 15:07:04 -06:00
Axel Kohlmeyer 5a341bee09 minor cleanup in docs and updated log files for kolmogorov/crespi/full 2018-03-23 06:42:04 -04:00
Axel Kohlmeyer c398eb6b57 update kolmogorov-crespi examples 2018-03-22 19:42:07 -04:00
Axel Kohlmeyer 8de7c449fc refactor code and examples to match LAMMPS conventions. whitespace cleanup. shorten examples. 2018-03-22 19:31:41 -04:00
oywg11 6415befb5b Add more examples 2018-03-14 16:30:54 +02:00
oywg11 bbb2a6d641 Finally updated the github tutorial 2018-03-13 17:43:25 +02:00
Axel Kohlmeyer fcfbdb13ab provide new reference outputs for various reaxff examples 2018-03-08 18:10:28 -05:00
Axel Kohlmeyer 52446eed6d make fix bond/react example inputs more similar to other input examples in LAMMPS 2018-03-03 19:34:31 -05:00
Jacob Gissinger 3b90f60064
Merge pull request #3 from lammps/master 
rebase
 2018-02-24 23:49:27 -07:00
jrgissing 7d1de34533 gatherv fix, doc updates 2018-02-24 22:49:28 -07:00
Axel Kohlmeyer 3787b89447 re-add compressed data file (was hidden by .gitignore) 2018-02-22 02:31:25 -05:00
Steve Plimpton aa1503b7e0
Merge pull request #800 from athomps/fix_gcmc_segfault_fix 
Added warning to discourage use of group all and fixed some segfault …
 2018-02-21 09:50:22 -07:00
Axel Kohlmeyer daae906162 move fix bond/react examples and compress large data file 2018-02-21 10:30:35 +01:00
Steven J. Plimpton c399b75dec 2nd try on LATTE error returns, plus a couple minor doc edits 2018-02-20 12:52:12 -07:00
jrgissing a04a975d3a add large nylon example for parallel validation, reformat doc page 2018-02-11 17:35:47 -07:00
Axel Kohlmeyer a6eb521468 strip off unwanted ^M characters 2018-02-09 17:32:32 +01:00
jrgissing 996c62f4e0 fix bond/react: generalized classical chemical reactions 2018-02-07 21:58:05 -07:00
Aidan Thompson 1d403b2aa3 Added warning to discourage use of group all and fixed some segfault cases 2018-02-05 13:29:14 -07:00
Axel Kohlmeyer 3e0cb9b463 rename examples to match usual naming conventions and add reference output. 2018-02-01 18:56:10 +01:00
Hendrik Heenen f7e2bf239f Added MOF-FF src, doc and example files 2018-01-21 11:40:48 +01:00
Steve Plimpton bf48f3e240
Merge pull request #758 from mkanski/ci-ReaxFF 
Modification of ReaxFF
 2018-01-16 13:04:20 -07:00
Steven J Plimpton 21ff4407ab update of COUPLE/simple examples 2018-01-16 10:48:38 -07:00
Stan Moore b374813104 Add reax example 2018-01-16 08:50:30 -07:00
mkanski e26c170679 Added example and tabulated close-range correction 2018-01-09 15:08:08 +01:00
Steve Plimpton 1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates 
Collected bugfixes and updates for the next patch release
 2018-01-08 09:20:18 -07:00
Axel Kohlmeyer 46217db8a5 make python functions examples more complete by adding exception handling and initializing variables 2018-01-06 12:56:42 -05:00
Richard Berger 2a131d1416 Merge remote-tracking branch 'upstream/master' into fix_python_move 2017-12-15 13:56:54 -05:00
Richard Berger bcc5f49d0b Rename fix python to fix python/invoke 2017-12-15 13:53:04 -05:00
Richard Berger 950bfb84a9 Clean up after renaming back to fix python/move 2017-12-15 13:27:27 -05:00
Richard Berger 4d725c3153 Revert "Rename fix python/move to move/python" 
This reverts commit 4d915dba08.
 2017-12-15 13:17:12 -05:00
Steve Plimpton 73d509f339
Merge pull request #735 from jaapkroe/extep 
Add ExTeP pair style
 2017-12-07 08:22:34 -07:00
Richard Berger 4d915dba08 Rename fix python/move to move/python 2017-12-05 23:42:57 -05:00
Richard Berger f8891a4451 Rename fix python/integrate to python/move 
This is to avoid confusion to what LAMMPS considers to be an
integrator like Verlet and RESPA.
 2017-12-02 01:04:46 -05:00
Giacomo Fiorin 51688b2504 Improve performance of Python integrator (NVE_Opt version) 
Removing the loop over atoms by using NumPy array indexing allows to recover
performance close to that of plain fix nve.
 2017-12-02 00:40:21 -05:00
Richard Berger 93be2d264e Detect correct integer type in lammps python interface 2017-12-02 00:39:15 -05:00
Richard Berger b9fd1156b2 Completed first version of fix python/integrate 
This includes an example of how to implement fix NVE in Python.

The library interface was extended to provide direct access to atom data using
numpy arrays. No data copies are made and numpy operations directly manipulate
memory of the native code.

To keep this numpy dependency optional, all functions are wrapped into the
lammps.numpy sub-object which is only loaded when accessed.
 2017-12-02 00:39:15 -05:00
Axel Kohlmeyer 5647522906 various small cosmetic adjustments to increase conformance with LAMMPS programming conventions 2017-11-28 12:34:23 -05:00
Axel Kohlmeyer e4b14213b4 delete old log files. new log files are approved by @athomps 2017-11-28 11:35:49 -05:00
Jaap Kroes 5770a20e2c added ExTeP to USER-MISC 2017-11-27 21:16:51 +01:00