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1047 Commits

Author SHA1 Message Date
Axel Kohlmeyer badfdd7433 download only the plumed-src package and include further tweaks to be compatible with plumed 2.5b 2018-11-03 00:21:10 -04:00
Axel Kohlmeyer ac11d66d5a provide reference logfiles and move generated files to reference folder 2018-11-02 23:28:09 -04:00
Ryan S. Elliott 1b98c0e40d Merge remote-tracking branch 'lammps/master' into kim-v2-update 2018-10-30 18:40:55 -05:00
Morteza Jalalvand ba6f6f73f1 first commit: added SDPD 2018-10-30 17:40:00 +03:30
Gareth Tribello ff9f836be4 Merge remote-tracking branch 'upstream/master' 2018-10-26 22:01:05 +01:00
Axel Kohlmeyer 1d38f2d725
Merge pull request #1165 from akohlmey/refactor-kspace-base-class 
Refactor kspace base class to have a settings() method
 2018-10-23 10:35:12 -04:00
Aidan Thompson 76a2a9ab0a Fixed normalization error for ordinate degree 2018-10-20 17:16:47 -06:00
Aidan Thompson 8223f5e0a3 Eliminated another initialization error and tweaked rdf-adf example 2018-10-20 16:46:45 -06:00
Axel Kohlmeyer 2140caa6f5 add an example for RDF and ADF computation with water molecules 2018-10-20 08:12:02 -04:00
Axel Kohlmeyer da84138475 correct scafacos input example 2018-10-19 15:31:53 -04:00
Ryan S. Elliott f61f43a56b Merge branch 'master' into kim-v2-update 2018-10-01 21:17:26 -05:00
Steve Plimpton 5a6226caa5 jive src headers with doc page entries and example scripts 2018-09-25 10:50:43 -06:00
Axel Kohlmeyer 44fcdc4024 update reference examples with versions that do not vary by MPI rank count 2018-09-06 21:20:47 -04:00
Axel Kohlmeyer 947f574503 Merge branch 'master' into compute_mop 
# Conflicts:
#	cmake/CMakeLists.txt
 2018-09-06 21:13:42 -04:00
Axel Kohlmeyer 0c92c22755 moved contents of USER-MOP package to USER-MISC as suggested by @sjplimp 2018-09-05 10:56:12 -04:00
Steve Plimpton d3d16882ca remove note for Rene 2018-09-05 08:12:19 -06:00
Richard Berger ff2e13e063 Merge branch 'master' into ScaFaCoS 2018-09-04 21:35:46 -04:00
Axel Kohlmeyer 1d3116d7c2 Merge branch 'master' into less-compiler-warnings 2018-09-04 08:59:12 -04:00
Axel Kohlmeyer cb4ffaf95c update docs and references for name changes in USER-MOP package, remove obsoleted files 2018-09-04 08:42:32 -04:00
RomainVermorel a797a0d193 changed computes names to stress/mop and stress/mop/profile 2018-09-04 14:02:19 +02:00
Axel Kohlmeyer f6f4b58167 add parallel reference output 2018-09-03 23:42:52 -04:00
Axel Kohlmeyer 7b423c6d4b integrate USER-MOP package into build and documentat system. apply latest LAMMPS programming style conventions 2018-09-03 23:37:25 -04:00
Axel Kohlmeyer 9e03bf7db9 make USER-DIFFRACTION input example fully consistent with output and remove additional input file 2018-09-01 19:12:46 -04:00
Steve Plimpton 5f0423b97d change -mpi to -mpicolor 2018-08-31 17:04:27 -06:00
Steve Plimpton 78301e5e93 Merge branch 'master' into cslib 2018-08-31 16:30:28 -06:00
Steve Plimpton f66ce801ad final testing 2018-08-31 16:21:45 -06:00
Steve Plimpton bc62002b1c units and doc changes 2018-08-31 16:05:24 -06:00
Steven J. Plimpton 83d453e78b updates to MD protocol and examples 2018-08-28 17:08:52 -06:00
Steven J. Plimpton 31ed3f7178 more changes to insure each triplet IJK computed exactly once 2018-08-27 17:09:59 -06:00
Steven J. Plimpton 44bda245a6 resolution of cutoff issues 2018-08-24 09:36:39 -06:00
Steven J. Plimpton 03b880a31c more doc page updates 2018-08-22 11:42:41 -06:00
Steven J. Plimpton 89a3670fb5 merge master into cslib branch, update docs 2018-08-22 11:19:55 -06:00
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