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1282 Commits

Author SHA1 Message Date
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
Richard Berger 9b703c6675 Fix file name 2019-08-20 16:54:37 -06:00
Richard Berger 2b42428d28 Extend lib interface to set fix external callback 
This allows creating a callback in Python and attaching it to
a fix external instance.
 2019-08-20 14:04:49 -06:00
Stan Moore 9a849a4d4f
Merge branch 'master' into master 2019-08-19 15:55:39 -06:00
charlie sievers ef3f382f61 fixed tbias 2019-08-07 17:27:35 -07:00
Ryan S. Elliott 8619462b3b Added logs for examples/kim 2019-08-07 16:14:22 -05:00
charlie sievers 131d5f0e69 Merge branch 'master' into lammps_gjf 2019-08-07 12:09:22 -07:00
charlie sievers f0f909996a Merge remote-tracking branch 'upstream/master' 2019-08-07 12:03:33 -07:00
Axel Kohlmeyer 5fd323fe32
simplify example folder for ilp/graphene/hbn potential 
- flatten directory structure
- remove CPU time and reduce excess precision from output
- delete redundant and unused files
- regenerate reference outputs
 2019-08-01 14:24:47 -04:00
Axel Kohlmeyer fa6a990536
reduce output precision to default and don't output per-step cpu time 2019-08-01 13:31:52 -04:00
oywg11 76bac4cedc Fix communication bug of ILP 2019-08-01 16:39:42 +03:00
oywg11 8f5cd8661f Fix communication bug of ILP 2019-08-01 16:38:19 +03:00
Stan Moore 602b4a47c0 Fix failing regression test 2019-07-30 10:37:27 -06:00
julient31 b5621b2c90 Merge branch 'master' of github.com:alxvov/lammps into OSO 
Conflicts:
	src/SPIN/neb_spin.cpp
 2019-07-30 09:14:49 -06:00
Axel Kohlmeyer 8fa4efa08e
Merge pull request #1440 from ellio167/kim-simulator-models 
Develop native support for KIM simulator models
 2019-07-30 10:53:58 -04:00
alxvov 9609c75073 Use descent condition, and no line search as a default option for 
all oso
 2019-07-30 11:16:40 +00:00
Axel Kohlmeyer 88523fdd6e
Merge pull request #1529 from rupertnash/compute_momentum 
add compute momentum command
 2019-07-29 22:51:29 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 7043b9f620
Merge pull request #1548 from jrgissing/bond/react-clarify-how-stabilization-works 
Bond/react clarify how stabilization works
 2019-07-29 19:55:24 -04:00
Ryan S. Elliott 0f059c56f9 Add details about installing models to KIM example input 2019-07-29 15:30:46 -05:00
casievers cc96ea1ded added respa compatability, and simplified examples 2019-07-25 15:23:01 -07:00
Ryan S. Elliott fadb40051b Update kim_query & clear and update examples/kim 2019-07-25 14:03:35 -05:00
casievers 13f4fe186b Updated examples/gjf/README.md 2019-07-24 16:30:02 -07:00
casievers b97e856bf2 Tally works and example readmes addes 2019-07-24 16:21:49 -07:00
casievers f4da632870 recent change to gjf tally (not working) 2019-07-24 16:21:49 -07:00
casievers e38072f365 added lammps python example 2019-07-24 16:21:49 -07:00
casievers 4a80edd75f updated fix_langevin and made example 2019-07-24 16:21:48 -07:00
alxvov f9ed12be4f modify line for spin_cubic, spin_none. edit docs a bit. 2019-07-24 23:21:07 +00:00
julient31 f1c3b9d0bf Commit2 JT 072319 
- corrected some mistakes in doc files
- modified oso examples to match new line options
 2019-07-23 11:24:52 -06:00
julient31 f0679cff6d Commit JT 072319 
- added 2 oso examples in examples/SPIN/spinmin
- added doc for oso_cg and oso_lbfgs
 2019-07-23 09:27:15 -06:00
Rupert Nash 243ce8dbfc
Merge branch 'master' into compute_momentum 2019-07-22 09:48:08 +01:00
Ryan S. Elliott 03d26f6f6f Merge branch 'master' into kim-simulator-models 2019-07-21 13:59:48 -05:00
Oliver Henrich c2643a519e Clarified explanation of new example3 2019-07-19 13:29:39 +01:00
Oliver Henrich 57fd9723a5 Added comment on new duplex3 2019-07-19 12:30:01 +01:00
Oliver Henrich 7bf9757755 Updated input and log files, amended comment in data files 2019-07-19 11:57:58 +01:00
Ryan S. Elliott 1f47da6c51 Add fixed_types to kim_init & split to kim_query 2019-07-08 17:46:47 -05:00
Rupert Nash 32728375b9 add test script for compute momentum 2019-07-01 13:39:32 +01:00
jrgissing af8103433c add stabilized vs unstabilized examples 2019-06-30 22:13:12 -06:00
Ellad Tadmor 483353a017 Merge remote-tracking branch 'lammps/master' into kim-simulator-models 2019-06-24 15:35:06 -05:00
Ryan S. Elliott c11caf4509 update kim examples to temp. current state of code 2019-06-23 10:34:43 -05:00
Ellad B. Tadmor 88994d813a Ignore kim.log in examples/kim 2019-06-21 18:38:48 -05:00
Ryan S. Elliott 0613c10395 Work on kim_style for latest definition prototype 2019-06-20 16:45:45 -05:00
Andrew Schultz 87e6fda820 Merge remote-tracking branch 'upstream/master' 2019-06-19 18:52:47 -04:00
Andrew Schultz 395a9d3739 Fold hma compute into USER-MISC 2019-06-19 16:12:15 -04:00
Steve Plimpton 0bc648e23e add message quit protocol, to allow for non-quantum MD steps 2019-06-18 14:30:30 -06:00
Axel Kohlmeyer e9666f585f
update log files for kolmogorov/crespi/full potential 2019-06-17 15:46:54 -04:00
Axel Kohlmeyer 92615bda3a
update kolmogorov/crespi/full example input for recent change in REBO 2019-06-17 07:38:11 -04:00
Axel Kohlmeyer daa53e3008
Merge pull request #1469 from julient31/pppm_spin 
Adding PPPM and Ewald solvers for electric dipoles and magnetic spins
 2019-06-12 14:50:18 -04:00
Andrew Schultz 45a2f9ae68 Merge remote-tracking branch 'upstream/master' 2019-06-10 16:15:07 -04:00
Axel Kohlmeyer c9fe5810c1
add log outputs for updated kim_style command input examples 2019-05-30 21:52:23 -04:00
Axel Kohlmeyer 24a63f0f31
update kim_style command semantics as discussed in PR #1440 
this also adds documentation of error messages in the kim_style header
 2019-05-30 21:51:13 -04:00
julient31 35be1724e3 Commit JT 052819 
- corrected examples in examples/SPIN/dipole_spin
- modified warning message in src/SPIN/pair_spin_dipole_*.cpp
 2019-05-28 15:31:03 -06:00
Axel Kohlmeyer b3a01694b7
remove leftover fix qeq/reax command 2019-05-27 23:34:05 -04:00
Axel Kohlmeyer 4619018ead
provide more simulator model variant input examples 2019-05-27 23:26:26 -04:00
Axel Kohlmeyer ce46d52c8a
add new 'kim_style' command as front end for KIM simulator (and regular) models 2019-05-24 10:23:26 -04:00
julient31 82b50706bd Commit2 JT 052019 
- some corrections in the examples
- deleted an old doc files (now redundant)
 2019-05-20 22:09:59 -06:00
julient31 e90eed9120 Commit JT 052019 
- deleted old doc
- renamed new doc files
 2019-05-20 21:48:05 -06:00
julient31 5f2f7d1575 Merge branch 'pppm_spin' of github.com:julient31/lammps into pppm_spin 2019-05-20 21:35:52 -06:00
julient31 3e60ec9be1 Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin 2019-05-20 21:35:16 -06:00
Axel Kohlmeyer 38a8c765f0
add support species checking 2019-05-20 22:54:20 -04:00
Axel Kohlmeyer 0349e9fee9
update/correct list of example folders 2019-05-20 15:08:33 -04:00
julient31 fbb78e7b78 Commit JT 051719 
- removed qsymp pair style
- cleaned doc (pair/spin/diole and kspace_style)
- cleaned kspace .cpp/h files
 2019-05-17 15:04:14 -06:00
julient31 0c0b106924 Commit2 JT 051519 
- started doc pair_spin_dipole.txt
- renamed all pair/spin/dipole
- created and tested example pair/spin/dipole/cut
 2019-05-15 20:49:05 -06:00
julient31 fd168068a1 Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin 
Conflicts:
	src/SPIN/fix_nve_spin.h
 2019-05-14 17:41:58 -06:00
Axel Kohlmeyer 2c51511325
update logfiles for SPIN package with cubic anisotropy 2019-05-14 15:49:41 -04:00
Axel Kohlmeyer 091dbfa265
Merge pull request #1457 from julient31/fix_cubic_aniso 
Adding a cubic anisotropy in the SPIN package, documentation corrections
 2019-05-14 15:08:21 -04:00
julient31 11f223416c Commit JT 051319 
- added a cubic anisotropy in fix_precession_spin
- added associated doc and examples
- corrected neb/spin commands in doc/src/
- added tools/spin/ description
 2019-05-13 16:59:39 -06:00
Steven Strong 805cc18b2d
Merge branch 'master' into e3b 2019-05-12 22:22:31 -05:00
Axel Kohlmeyer 2f580380a4
adjust drip potential example for new requirements for pair style rebo. recreate log files 2019-05-09 12:29:38 -04:00
Axel Kohlmeyer 47cf17e5c8
Merge branch 'master' into pair_drip 2019-05-09 12:19:41 -04:00
Steven Strong da75fc3eaa incorporate compute_pe_e3b into compute_pair 2019-05-08 09:05:09 -05:00
Mingjian Wen db54b03751 Force line length to 80 2019-05-04 22:55:22 -05:00
Mingjian Wen 24e41bc085 Update doc and examples due to the change of parameters 2019-05-04 22:24:05 -05:00
Axel Kohlmeyer fd3eade6d2
update reference date and examples for changes in REBO 2019-05-04 20:42:36 -04:00
Axel Kohlmeyer c2b2be5d6f
Merge branch 'master' into github-rebo-bugfix 2019-05-04 19:09:52 -04:00
Ryan S. Elliott 99430767df Start devel of native support for KIM simulator models 
* CMake change to use KIM-API SimulatorModels branch
* Minimal changes to pair_kim to illustrate use of KIM API
  interface. Only c++ interface is implemented for development.
* Added example input: in.kim.simulator-model
 2019-04-30 21:48:50 -05:00
Axel Kohlmeyer 8d9697dbf6
Merge pull request #1420 from dsbolin/gran_mods 
Updates and bugfixes to GRANULAR package
 2019-04-29 14:16:25 -04:00
Axel Kohlmeyer f052509015
Merge pull request #1421 from julient31/gneb_spin 
Adding a GNEB implementation in the SPIN package
 2019-04-29 14:14:58 -04:00
julient31 97baee4931 Commit2 JT 042919 
- modified energy/torque tolerance for faster convergence in
examples/SPIN/gneb/skyrmion/in.gneb.skyrmion
 2019-04-29 08:23:57 -06:00
Axel Kohlmeyer 98daf8f825
optimize granular examples and include logs 2019-04-29 09:48:57 -04:00
Axel Kohlmeyer 795cdf456f
simplify example and skip the system generation step, so it gives consistent results in serial and parallel 2019-04-25 19:02:35 -04:00
julient31 7c3f619e13 Commit JT 042519 
- moved examples/SPIN/gneb/interpolate/ toward
tools/spin/interpolate/gneb
- added gneb in the command files in doc/src
- modified the error messages in neb_spin.h/cpp
 2019-04-25 09:18:33 -06:00
julient31 a696b26301 Merge branch 'clean-master2' of github.com:julient31/lammps into pppm_spin 
Conflicts:
	src/SPIN/pair_spin_exchange.cpp
	src/atom.cpp
	src/pair.cpp
 2019-04-19 15:02:25 -06:00
Mingjian Wen ba7882c1ff Add parameter file and example 2019-04-19 14:17:57 -05:00
Steven Strong 69e7a2a237 add e3b water model 2019-04-16 11:32:47 -05:00
Dan S. Bolintineanu d0826f2838 Added granular example input scripts 2019-04-13 23:52:30 -06:00
julient31 70c816aa02 Commit JT 041019 
- corrected setforce/spin
- added an example
- added the documentation (in setforce)
- updated the Howto_spin documentation
 2019-04-10 13:18:33 -06:00
Dan S. Bolintineanu 4af22a723d Fixes several bugs in fix wall/gran, wall/gran/region: 
1. Radius of curvature for curved regions was incorrectly used to compute wall-particle overlaps
2. Uninitialized values of rolling and twisting history could produce crashes in
cases that don't initialize these to 0 by default. These are now initialized to 0.
3. Fixed a bug with the use of 'NULL' for specification of the tangential stiffness for
wall/gran and wall/gran/region
 2019-04-09 16:40:49 -06:00
julient31 814b9b9378 Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin 2019-04-08 11:26:48 -06:00
julient31 1501e9ba8a Commit3 JT 040819 
- README and interpolate.c for in examples/SPIN/gneb/interpolate/
 2019-04-08 11:22:02 -06:00
Dan S. Bolintineanu 1e07ef6f87 Added example for pouring of particles on flat wall with new granular pair style 2019-04-08 09:13:22 -06:00
julient31 da16a7e50b Commit JT 040519 
- initial rotation with Rodrigues' formula + exception
- worked on neb_spin documentation
- removed pair/spin warning for neb/spin
 2019-04-05 13:22:46 -06:00
Risto Toijala 619c2322e5 Merge remote-tracking branch 'upstream/master' into fix-elstop 2019-04-04 10:03:36 +03:00
Risto Toijala 0d78c7b43d fix elstop: Rename to fix electron/stopping 2019-04-04 09:57:15 +03:00
julient31 e45e92b1cb Commit JT 040319 
- improved examples
- start rework gneb init. (Rodrigues' formula)
 2019-04-03 11:24:37 -06:00
Axel Kohlmeyer 778537e734
update micelle example for improved reproducibility 2019-04-02 22:32:15 -04:00
julient31 0b8332cedf Commit2 JT 040119 
- improved verbose output
- work on examples
 2019-04-01 17:52:59 -06:00
julient31 677974573a Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin 2019-04-01 16:12:11 -06:00
Andrew Schultz bbec50bef1 Add HMA examples 2019-03-29 15:06:49 -04:00
Axel Kohlmeyer 2ad9355140
Merge pull request #1383 from akohlmey/final-changes-for-patch 
Several small changes and tweaks for patch release
 2019-03-27 17:00:56 -04:00
Axel Kohlmeyer c4fd658e9d
rename micelle-rigid to micelle.rigid 2019-03-27 11:07:14 -04:00
Axel Kohlmeyer 1926c95625
correct micelle data file without overwriting the molecule ids 2019-03-26 19:08:58 -04:00
Axel Kohlmeyer dbd458e9e3
update micelle example with corrected data file and rigid body input 2019-03-26 16:35:35 -04:00
Axel Kohlmeyer 5a6a8a9e57
Merge pull request #1379 from lammps/hyper 
Hyper-dynamics update
 2019-03-26 16:30:37 -04:00
julient31 b8747ce8fb Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin 
Conflicts:
	doc/src/min_modify.txt
	doc/src/min_spin.txt
	examples/SPIN/spinmin/in.spinmin.bfo
	examples/SPIN/spinmin/in.spinmin.iron
	src/SPIN/fix_precession_spin.cpp
	src/SPIN/min_spin.cpp
	src/SPIN/min_spin.h
	src/SPIN/pair_spin_dmi.cpp
	src/SPIN/pair_spin_exchange.cpp
 2019-03-26 10:59:21 -06:00
Risto Toijala 8c99752cec Add fix elstop to USER-MISC 
Implements inelastic energy loss for fast particles in solids.
 2019-03-26 10:08:20 +02:00
julient31 81a4d293db Commit4 JT 032519 
- corrected documentation (errors in min_spin.txt and
min_modify.txt)
- changed the code accordingly
 2019-03-25 15:43:58 -06:00
julient31 30be5e94d9 Commit3 JT 032519 
- updated the README file
- updated examples/SPIN/spinmin/
 2019-03-25 14:22:16 -06:00
julient31 7a00997a14 Commit2 JT 032519 
- added equations for documentation
- updated examples (not calling fix nve/spin)
- replaced error message by warning in all pair/spin
 2019-03-25 14:03:28 -06:00
julient31 a726362888 Commit JT 032519 
- adding all min files into new branch
- preparing branch for pull request of spin minimizer
 2019-03-25 12:57:42 -06:00
Steve Plimpton de99dc8974 new output files 2019-03-25 09:54:28 -06:00
Steve Plimpton e9384b6b17 updating output files 2019-03-25 09:52:16 -06:00
Ryan S. Elliott 3464464ea9 Update kim example query and log files 2019-03-22 20:20:47 -05:00
julient31 2cbf56846a Commit JT 032019 
- moved gneb files from src/REPLICA to src/SPIN
- changed name of min/spin
- implemented read_param in min.cpp and min_spin.cpp
- set sp_flag tests in min_spin.cpp and neb_spin.cpp
 2019-03-20 10:41:36 -06:00
Axel Kohlmeyer 741a7fe630
final touches to support compiling with libcurl transparently 2019-03-19 15:40:49 -04:00
julient31 0d4dbb8d73 Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin 2019-03-19 09:01:27 -06:00
julient31 033a5c2721 Commit JT 031419 
- cleaned fix_neb_spin
- first working version
 2019-03-14 11:07:24 -06:00
Steve Plimpton aca8ce1f53 Merge branch 'master' into hyper 
sync with GH master
 2019-03-13 12:19:06 -06:00
julient31 f6fb8b220d Commit 2 JT 031219 
- modified examples (gneb and spinmin now distinct)
- started documention for spinmin
 2019-03-12 16:59:13 -06:00
julient31 cc2b5fbb80 Commit JT 031119 
- add min_post_force in precession
 2019-03-11 17:37:44 -06:00
julient31 5fff18932d Commit 2 JT 031119 
- new input files gneb and spinmin
 2019-03-11 13:23:55 -06:00
julient31 14a00662e6 Commit JT 031119 
- first working version of spinmin
 2019-03-11 13:04:03 -06:00
julient31 edd4b0cf25 Commit JT 030419 
- added minspin
- modifs before co
 2019-03-04 07:35:02 -07:00
Steve Plimpton f0ec2e3279 refactoring of global and local hyper, including amended doc pages 2019-03-01 18:47:34 -07:00
Axel Kohlmeyer c555f7e2ed
update permissions 2019-02-28 17:52:53 -05:00
Axel Kohlmeyer 14e6c126a8
Merge pull request #1314 from charlessievers/OptimizedDynamicalMatrix 
add command to compute the Dynamical Matrix
 2019-02-28 17:08:36 -05:00
Axel Kohlmeyer 7062bc862e
remove third_order command and ASE based examples to be added in a new pull request 2019-02-28 15:21:48 -05:00
Axel Kohlmeyer 286112ffbc
count each force computation as one simulation step. this avoids accessing uninitialized data, too. 2019-02-28 11:00:55 -05:00
Axel Kohlmeyer 326a97624e
Merge pull request #1317 from ornladios/adios2-master 
USER-ADIOS package with ADIOS 2.x
 2019-02-27 17:24:12 -05:00
Axel Kohlmeyer 73401d02c0
convert a couple of inputs from using pair style reax to reax/c 2019-02-27 16:08:41 -05:00
Axel Kohlmeyer e6df92e65a
Merge pull request #1011 from ellio167/kim-v2-update 
KIM v2 update
 2019-02-21 20:06:59 -05:00
Norbert Podhorszki 3ad268739b Add dump adios to PDF build. Update example config with better documentation 2019-02-20 17:02:48 -05:00
Norbert Podhorszki 2de01cef45 Dump atom/adios and dump custom/adios command notifications 2019-02-20 16:21:07 -05:00
Norbert Podhorszki a4b9542ba9 remove personal runconf file. cleanup ADIOS2 xml config file for example 2019-02-20 09:02:24 -05:00
Norbert Podhorszki 410d79d8b7 Add an example for USER/adios based on the balance example 2019-02-20 09:02:24 -05:00
pmla 35d2de298f added license information to all files 
updated documentation
added example file
added graphene structure
 2019-02-15 18:49:23 -05:00
casievers 4b8621e7ef Added additional tutorials for the dynamical matrix calculator 2019-02-11 19:46:22 -08:00
Ryan S. Elliott 6068a719ff Updated example/kim/log.* files 2019-02-06 23:53:47 -06:00
julient31 9fcd69921f Commit JT 020419 
- neb/spin implemneted
- rotational initial states to be implemented
- climbing image to be implemented
 2019-02-04 11:27:00 -07:00
Ryan S. Elliott d677335b23 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-02-03 12:45:44 -06:00
charlie sievers adebe90315 Optimized Dynamical Matrix 2019-02-01 21:55:29 -08:00
Axel Kohlmeyer 7606529f03
Merge pull request #1302 from akohlmey/combined-user-fep-soft-updates 
Combined USER-FEP related updates
 2019-01-31 22:57:51 +01:00
Axel Kohlmeyer a93d8dda3c add example input and logfiles for using fix qeq/shielded with pair style reax/c 2019-01-31 14:14:29 +01:00
PabloPiaggi ccdfde4978 Update example log file 2019-01-30 15:16:35 +01:00
julient31 08b1728a96 Commit JT 012919 
- commit tuesday evening, second day imp.
- dev. fix_neb_spin
 2019-01-29 13:05:03 -07:00
Axel Kohlmeyer 536e34974a Merge branch 'soft_class2_potentials' of https://github.com/evoyiatzis/lammps into combined-user-fep-soft-updates 2019-01-24 15:33:30 +01:00
Steven Vandenbrande 60b137f241 Add examples for the USER-YAFF package 2019-01-22 10:09:10 +01:00
Ryan S. Elliott 23ce00f366 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-01-16 21:49:14 -06:00
Evangelos Voyiatzis 1dbdadcf89
Add files via upload 2019-01-14 09:53:10 +01:00