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1115 Commits

Author SHA1 Message Date
Rene Halver c23534019c fixed typo in example file name 2018-08-21 17:28:42 -06:00
Ryan S. Elliott d0667d21cc Merge branch 'master' into kim-v2-update 2018-08-18 12:23:19 -05:00
Rene Halver e08aaa7e39 added examples for P3M with ScaFaCoS 2018-08-08 15:03:47 -06:00
Rene Halver 2a5e550bda updated log files 2018-08-08 15:02:19 -06:00
Rene Halver 7f5476b408 removed deprecated log files (will be replaced with more current ones) 2018-08-08 14:04:41 -06:00
Rene Halver 74633ce28f fixed merge conflict 2018-08-08 09:53:27 -06:00
Rene Halver cdde51d8af fixed example so that P3M also works, changed tolerance type in the FMM example 2018-08-07 14:29:04 -06:00
sergeylishchuk 4d75d2d611 more changes to ATM source and doc file 2018-08-06 20:49:05 +01:00
Steven J. Plimpton 5789ef9128 bug-fix for slope() function in variable 2018-08-03 10:08:02 -06:00
Christoph Junghans 463e34cef5 Merge remote-tracking branch 'origin/master' into HEAD 2018-08-03 08:13:12 -06:00
Steven J. Plimpton b2d1332d46 change proc count to color for MPI_Comm_split 2018-08-02 14:47:20 -06:00
Axel Kohlmeyer d877a12e0c Merge branch 'fix_xrd_histo' of https://github.com/king-michael/lammps into collected-small-fixes 2018-08-01 13:57:56 +02:00
Michael King c8be5a3f2d change ave/histo to ave/histo/weight 2018-08-01 11:11:18 +02:00
julient31 28993d9823 Commit JT 072618 
- improvements documentation (dmi and exchange)
- correction error cross product in pair_spin_dmi.cpp
- implementation mech. part in pair_spin_dmi.cpp
- correction in all pairs: init_one for [j][i] couples
- correction in atom_vec_spin.cpp: index error in read_data
- some improvements in pair_spin_dmi.cpp and pair_spin_magelec.cpp
 2018-07-27 12:00:15 +02:00
sergeylishchuk 7cae80b6d8 Merge https://github.com/lammps/lammps 
more changes to ATM source and doc file
 2018-07-26 11:42:53 +01:00
Steven J. Plimpton b2c75cc0b9 enable LAMMPS/VASP coupling to work w/out using VASP 2018-07-24 17:29:52 -06:00
Steven J. Plimpton a4dbac63d3 more updates to the new MESSAGE package 2018-07-24 17:22:15 -06:00
Steven J. Plimpton ab1cc706cc change syntax of standard C include files 2018-07-24 11:55:56 -06:00
Rene Halver ae2d43031b added pressure output, to compare results with global virial (with internal PPPM) 2018-07-23 16:25:02 -06:00
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
Ryan S. Elliott 6ab93b52bc Merge remote-tracking branch 'lammps/master' into kim-v2-update 2018-07-23 09:30:43 -05:00
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
Ryan S. Elliott 3e73418601 Updated example/kim log files 2018-07-11 15:09:58 -07:00
Ryan S. Elliott fcec1498e3 update input example scripts for pair_kim 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 7eeb96f1af Update pair_kim to work with new neig. list Hints 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 0264e044e2 Update example/kim input files 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 5bdc295331 Add skin to pair_kim neigh-list cutoffs & update docs 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 68ec8822ee Update example/kim/log.* 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 955fe583d8 Updated docs for new pair_kim 2018-07-11 15:09:57 -07:00
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
Axel Kohlmeyer adbc75cae6 add alternate log files with the latest version of LAMMPS 2017-11-13 11:52:01 -05:00
Steve Plimpton dde94c28a7 new example scripts for fix gcmc 2017-11-13 09:07:25 -07:00
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
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
Axel Kohlmeyer ac6434e496 add input examples for custom rigid body definition 2017-10-20 13:54:45 -04:00
vishalkenchan e284545c5b added some documentation and reference example 2017-10-20 12:03:22 +02:00
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
Ulf R. Pedersen 957263431a Ensure consistency with documentation 2017-10-04 09:38:43 +02:00
Axel Kohlmeyer f07719e924 make fix rhok examples more consistent with LAMMPS conventions: 
- move example folder to examples/USER/misc/
- comment out writing of trajectory files
- reduce run length (for easier testing for regressions)
- record example outputs for 1 and 4 MPI processes
- rename readme.md to README.md for visibility
 2017-10-03 10:08:38 -04:00
Ulf R. Pedersen 5f527091b8 Update readme.md 2017-10-03 12:02:01 +02:00
Ulf R. Pedersen 30aaa7e47b Update readme.md 2017-10-03 12:00:43 +02:00
Ulf R. Pedersen 74dcf0bf9b Update readme.md 2017-10-03 11:54:46 +02:00
Ulf R. Pedersen e9b07a7a10 Update readme.md 2017-10-03 11:52:48 +02:00
Ulf R. Pedersen fd8f5f8f9e Update readme.md 2017-10-03 11:52:08 +02:00
Ulf R. Pedersen 5c59eb637b Update readme.md 2017-10-03 11:49:57 +02:00
Ulf R. Pedersen 250ef9f837 Update readme.md 2017-10-03 11:46:08 +02:00
Ulf R. Pedersen e44f370d49 Update readme.md 2017-10-03 11:44:52 +02:00
Ulf R. Pedersen 1e790fbafe Update readme.md 
Now use the standard namings.
Corrected spelling errors.
 2017-10-03 11:44:23 +02:00
Ulf R. Pedersen 35cc795972 Update in.setup 2017-10-03 11:17:43 +02:00
Ulf R. Pedersen 245bf74552 Rename setup.lmp to in.setup 2017-10-03 11:16:54 +02:00
Ulf R. Pedersen 7e8bbe8481 Rename pinning.lmp to in.pinning 2017-10-03 11:16:29 +02:00
Ulf R. Pedersen e6d687faac Rename crystal.lmp to in.crystal 2017-10-03 11:15:49 +02:00
David Nicholson 1dffb0cf82 reran npt_biaxial examples 2017-10-02 23:27:10 -04:00
Axel Kohlmeyer 00aef0fe00 rerun logfiles for USER-UEF example inputs 2017-10-02 17:40:46 -04:00
David Nicholson 4ef63feea7 reran examples 2017-09-29 15:50:31 -04:00
David Nicholson 855b6000ef initial commit. doc is in the works 2017-09-28 16:34:18 -04:00
Ulf R. Pedersen 34c1adb4dd Merge https://github.com/lammps/lammps 2017-09-28 12:28:58 +02:00
Ulf R. Pedersen f1aea57e30 Update readme.md 2017-09-25 18:48:21 +02:00
Ulf R. Pedersen b35f2ff8b4 Example of Interface Pinning Computation 2017-09-25 18:44:24 +02:00
Steve Plimpton ee487ef4aa Merge pull request #652 from junghans/latte 
Add LATTE fix
 2017-09-22 10:32:19 -06:00
Steve Plimpton a8ae886667 update fix latte examples and virial 2017-09-21 10:40:54 -06:00
Ulf R. Pedersen 3381a43378 Added readme.m 2017-09-21 16:20:06 +02:00
Ulf R. Pedersen 73708b091c Added readme file, and removed old files 2017-09-21 16:17:26 +02:00
Christian Negre 5e35ab251b fixed sucrose 2017-09-20 17:11:49 -06:00
Axel Kohlmeyer ad25a95297 whitespace cleanup 2017-09-20 11:13:13 -04:00
Axel Kohlmeyer e7d042ba1a convert DOS/Windows CR-LF line endings to native format 2017-09-20 11:12:58 -04:00
Steve Plimpton dd49d54889 new SNAP potentials and examples 2017-09-20 08:54:30 -06:00
Steve Plimpton ac897ea645 LATTE package doc update and some small code changes 2017-09-19 16:27:25 -06:00
Axel Kohlmeyer 5f1842829e activate virial contribution in `fix lb/rigid/pc/sphere` by default and protect virial computation with evflag 2017-09-17 21:10:41 -04:00
Christoph Junghans 2f6be88c4a Merge remote-tracking branch 'origin/master' into exaalt 2017-09-08 07:04:12 -06:00
Richard Zamora 7b1542a0ba merging stable and exaalt branches into exaaltstable 2017-09-07 16:31:50 -06:00
Steve Plimpton 4161868bcf Merge pull request #640 from ohenrich/user-cgdna 
USER-CGDNA - sequence-dependent stacking and h-bonding strength
 2017-09-06 08:52:05 -06:00
Steve Plimpton b170606052 Merge pull request #620 from amilumas/master 
Temper_NPT
 2017-09-05 10:08:55 -06:00
Oliver Henrich 12fe614ddf Added sequence-dependent stacking and base-pairing strength 2017-09-05 10:48:38 +01:00
Axel Kohlmeyer 4d2ed30b35 add reference outputs to temper/npt example 2017-08-31 14:13:02 -04:00
Axel Kohlmeyer f3dda30f8e fully integrate temper/npt command into manual 2017-08-31 13:53:40 -04:00
Julien Devemy a5b65c1af4 Mods for extra/special/per/atom and add toluene 2017-08-31 15:03:04 +02:00
Amulya 6a4bbddb3b Add files via upload 
data file for example
 2017-08-28 14:56:37 -04:00
Amulya 2add18e013 Create in.temper_npt 
example for temper/npt
 2017-08-28 14:55:43 -04:00
Steve Plimpton f945d4567d new USER-MESO package 2017-08-18 17:33:42 -06:00
Axel Kohlmeyer 7d0d701eaf add reference outputs for QUIP/GAP example 2017-07-28 16:05:16 -04:00
Axel Kohlmeyer 85120842dd update QUIP examples to closer match typical LAMMPS examples 2017-07-28 15:20:33 -04:00
Axel Kohlmeyer da7a5f55d3 Merge branch 'kim-install' into install-and-docs-reviewed 2017-07-26 19:32:55 -04:00
sjplimp 1ddace4dba Merge pull request #595 from libAtoms/idces2quip 
Add a (contrived) molecular example for USER-QUIP
 2017-07-24 08:55:03 -06:00
Max Veit 1afab981b0 Clarified some points in in.molecular example 2017-07-22 14:40:33 +01:00
Axel Kohlmeyer 1af937e99d Update in.molecular 
- expand comments to provide more details on the choice of exclusion settings
- comment out dump file generation
 2017-07-21 22:00:29 -04:00
Max Veit 4e0a249e27 Add a (contrived) molecular example for USER-QUIP 
This example showcases the use of different 'special_bonds' settings for
different pair styles, so quip gets all the bonded neighbours but lj can
exclude them if it needs to.

The results have been checked against a pure quip implementation of the
potential; the expected lammps output is included.

DISCLAIMER: This example mixes parameters for methane and silane and is
NOT intended to be a realistic representation of either system.
 2017-07-22 01:33:15 +01:00
Axel Kohlmeyer b1b399d5c3 update readme for examples 2017-07-21 15:06:15 -04:00
Steve Plimpton 59db5f6a17 update of Fortran-DFTB interface to be compatible with fix msst 2017-07-20 14:40:35 -06:00
sjplimp 3cd597e948 Merge pull request #585 from akohlmey/make-py-manual-cleanup 
Make.py removal and manual cleanup
 2017-07-20 12:05:04 -06:00
Axel Kohlmeyer bdd2f3a6b2 remove references to Make.py and USER-CUDA 2017-07-20 12:25:42 -04:00
Axel Kohlmeyer 49b4cf9a77 remove references to Make.py and USER-CUDA 2017-07-18 13:24:32 -04:00
Axel Kohlmeyer d9186c8fde Revert "use neighbor list exclusions instead of a zero cutoff" 
This reverts commit bbb4d63db9.
 2017-07-18 01:17:34 -04:00
Steve Plimpton 296e572e69 better Install.py script for KIM from Ryan Elliott 2017-07-14 16:25:16 -06:00
Axel Kohlmeyer bbb4d63db9 use neighbor list exclusions instead of a zero cutoff 2017-07-14 14:52:08 -04:00
Axel Kohlmeyer 1c92eecea7 move updated gauss_flow example to the correct folder 2017-07-14 14:01:41 -04:00
Axel Kohlmeyer 14f1d646ad provide working examples for all four peridynamics models and reference outputs 2017-07-14 13:46:19 -04:00
Axel Kohlmeyer 4d4c03a1e4 restore gaussian flow example that was lost. tweak input to make it usable for comparing 2017-07-14 12:33:40 -04:00
sjplimp 9988030409 Merge pull request #563 from akohlmey/airebo-example 
Add AIREBO and AIREBO-M example input deck
 2017-07-13 13:12:30 -06:00
sjplimp a3a0c9b144 Merge pull request #570 from akohlmey/collected-small-changes 
Collected small changes
 2017-07-13 11:26:47 -06:00
sjplimp e58bcd8b4a Merge pull request #568 from akohlmey/fix_gcmc_parallel_workaround 
Workaround for data corruption when using fix gcmc in parallel with shake or fix rigid
 2017-07-13 11:23:49 -06:00
sjplimp d3a45f6d50 Merge pull request #560 from aershadinia/master 
EES wall potential
 2017-07-13 11:22:47 -06:00