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1401 Commits

Author SHA1 Message Date
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
Evangelos Voyiatzis 7a4b6526de
Create in.deletion 2019-01-14 09:52:28 +01:00
Evangelos Voyiatzis 16b8c94aae
Add files via upload 2019-01-14 09:49:37 +01:00
Evangelos Voyiatzis 62b4c69360
Create in.insertion 2019-01-14 09:48:40 +01:00
Evangelos Voyiatzis 261122d59c
Update README 2019-01-14 09:43:13 +01:00
julient31 7a2d326103 Commit JT 010819 
- commit before co
 2019-01-08 09:19:49 -07:00
Axel Kohlmeyer 7323179de3 rename pair style lebedeva to lebedeva/z to be consistent with kolmolgorov/crespi/z 2019-01-03 17:30:16 -05:00
Axel Kohlmeyer 41ccf832bf update log files 2018-12-30 04:30:58 -05:00
Axel Kohlmeyer 6d5ab3dac1 Merge branch 'github-rebo-bugfix' of https://github.com/CF17/lammps into test-rebo 
# Conflicts:
#	examples/airebo/log.23Jun17.airebo-m.g++.1
#	examples/airebo/log.23Jun17.airebo-m.g++.4
#	examples/airebo/log.23Jun17.airebo.g++.1
#	examples/airebo/log.23Jun17.airebo.g++.4
#	examples/airebo/log.27Nov18.airebo-m.g++.1
#	examples/airebo/log.27Nov18.airebo-m.g++.4
#	examples/airebo/log.27Nov18.airebo.g++.1
#	examples/airebo/log.27Nov18.airebo.g++.4
#	examples/airebo/log.29Jun18.airebo-m.g++.1
#	examples/airebo/log.29Jun18.airebo-m.g++.4
#	examples/airebo/log.29Jun18.airebo.g++.1
#	examples/airebo/log.29Jun18.airebo.g++.4
 2018-12-30 03:44:38 -05:00
Axel Kohlmeyer 444dcca433
Merge pull request #1254 from akohlmey/remove-reax-meam 
Remove REAX and MEAM packages
 2018-12-29 13:06:07 -05:00
Axel Kohlmeyer 9355e7e5cc
Merge pull request #1243 from athomps/snap-foundtest 
Removed redundant element list from pair_coeff snap syntax
 2018-12-29 13:04:47 -05:00
Ryan S. Elliott 6c0b100a53 Merge branch 'master' into kim-v2-update 2018-12-16 15:56:33 -06:00
Ryan S. Elliott b068690e13 Update for kim-api beta.3 release 2018-12-12 16:21:54 -06:00
Axel Kohlmeyer 96c7f256f9 Merge branch 'snap-foundtest' of https://github.com/athomps/lammps into collected-post-stable-patches 2018-12-12 00:16:36 -05:00
Axel Kohlmeyer 02bdda0d05 Merge branch 'remove-reax-meam' into collected-post-stable-patches 2018-12-12 00:14:58 -05:00
Axel Kohlmeyer be3c80829a Merge branch 'collected-small-changes' into collected-post-stable-patches 2018-12-12 00:14:41 -05:00
Axel Kohlmeyer 0a610cb482 Merge branch 'sllod' into collected-post-stable-patches 2018-12-12 00:14:33 -05:00
Axel Kohlmeyer d15e4b1546
Merge branch 'master' into remove-reax-meam 2018-12-11 23:31:48 -05:00
Axel Kohlmeyer bbe863f1ac add input for controlling a wall for a slab 2018-12-11 05:43:19 -05:00
Axel Kohlmeyer eeaeab0832 add example for using fix controller with a moving wall to adjust pressure 2018-12-11 05:31:12 -05:00
Axel Kohlmeyer 0b5c273e2d update examples for removal of reax and meam 2018-12-10 15:16:34 -05:00
Axel Kohlmeyer b6b813459b update example logfiles for USER-DRUDE package 2018-12-10 11:04:52 -05:00
Axel Kohlmeyer 998a512143 update log files for USER-UEF 2018-12-07 10:19:34 -05:00
Axel Kohlmeyer e61b553bb3 update USER-MOFF log files 2018-12-07 05:54:02 -05:00
Axel Kohlmeyer 20eca799b1 update log files for USER-DIFFRACTION package 2018-12-07 05:50:39 -05:00
Axel Kohlmeyer 8ce60d8761 update USER-CGSDK and USER-COLVARS log files 2018-12-07 05:03:26 -05:00
Axel Kohlmeyer 685a8bfc62 update or add logs for USER-AWPMD, USER-BOCS, and USER-CGDNA 2018-12-07 04:32:46 -05:00
Axel Kohlmeyer cd0924ca4c add log files for USER-AWPMD examples 2018-12-07 03:49:46 -05:00
Axel Kohlmeyer 18f7e96e8a update log files for USER-PLUMED examples 2018-12-06 19:07:36 -05:00
Axel Kohlmeyer e01ba84fd2 update log files for USER-SCAFACOS 2018-12-06 19:01:20 -05:00
Aidan Thompson fa7e02ea71 Removed redundant element list from pair_coeff snap syntax 2018-12-03 20:28:01 -07:00
Axel Kohlmeyer 55077cea4d Merge branch 'lebedeva2' of https://github.com/zbych127/lammps into collected-post-stable-patches 2018-12-03 15:24:31 -05:00
Ronald E. Miller 01f47c4450 fixed the input for the example 2018-11-29 20:06:36 -05:00
Ronald E. Miller 4d06e11cfd creating clean fix npt/cauchy package and docs 2018-11-29 19:55:31 -05:00
Axel Kohlmeyer 5d2730f055 update log files for rigid, shear, snap, srd, streitz, threebody, vashsista, and voronoi examples 2018-11-29 18:22:18 -05:00
Axel Kohlmeyer 4b8c6d40e2 update log files for qeq and rdf-adf examples 2018-11-29 15:15:14 -05:00
Axel Kohlmeyer 46bf4b7efb update log files for peptide, peri, pour and python examples 2018-11-29 14:51:25 -05:00
Axel Kohlmeyer cef4164460 update log files for min, msst, nb3b, nemd, and obstacle examples 2018-11-29 14:13:11 -05:00
Axel Kohlmeyer 074a9663cb update log files for melt and micelle example 2018-11-29 14:05:28 -05:00
Axel Kohlmeyer d67dad9d67 update log files for meam examples 2018-11-29 12:47:15 -05:00
Axel Kohlmeyer 41e24f6e8b update log files for gcmc example 2018-11-29 12:35:07 -05:00
Axel Kohlmeyer c763916f9e update log files for granregion hugoniostat and indent examples 2018-11-28 21:21:54 -05:00
Axel Kohlmeyer 48a408bb19 update log files for friction example 2018-11-28 18:42:48 -05:00
Axel Kohlmeyer 8e07aaf005 update log files for ellipse and flow examples 2018-11-28 16:16:19 -05:00
Axel Kohlmeyer 4a8f1a7a08 update log files for eim example 2018-11-28 16:11:15 -05:00
Axel Kohlmeyer 37289f7476 update log files for dipole and dreiding example inputs. add running some MD steps for dreiding 2018-11-28 16:07:12 -05:00
Axel Kohlmeyer 3ce61c42d6 update log files for crack and deposit examples 2018-11-28 16:01:42 -05:00
Axel Kohlmeyer 98c8f22046 update log files for coreshell examples 2018-11-28 15:56:58 -05:00
Axel Kohlmeyer 296cab0b09 update log files for controller example 2018-11-28 15:40:14 -05:00
Axel Kohlmeyer ab924e4f1d update log files for comb examples 2018-11-28 15:38:11 -05:00
Axel Kohlmeyer 852916983a update logs for colloid example 2018-11-28 14:53:29 -05:00
Axel Kohlmeyer d0a83e9e12 update cmap example logfiles 2018-11-28 14:51:19 -05:00
Axel Kohlmeyer 2ed90c1669 update log files for body examples 2018-11-28 14:46:47 -05:00
Axel Kohlmeyer c428088554 update logfiles for balance examples 2018-11-28 14:40:20 -05:00
Axel Kohlmeyer 77e7362168 update log files for airebo and atm examples 2018-11-28 14:28:20 -05:00
Zbigniew Koziol 2d0d08093b Another attempt to add Lebedeva potential 2018-11-28 09:33:44 +01:00
Axel Kohlmeyer a91d89b516 avoid array overflows and silence compiler warnings from unused parameters 2018-11-21 09:24:10 -05:00
Axel Kohlmeyer dcffeb546f update AIREBO/REBO examples and provide references for rebo and airebo with LJ and TORSION turned off 2018-11-20 13:56:46 -05:00
Axel Kohlmeyer 9f960baa4f restore USER-ATM package data files taken from CVS repo 2018-11-20 09:17:02 -05:00
Axel Kohlmeyer a7bfb30043 update atc/cauchy_born examples with missing files 2018-11-16 23:03:47 -05:00
Axel Kohlmeyer d0235dd018 remove cauchystat changes from fix_nh.cpp/.h/.txt (again). delete misplaced example that came back from the dead, too. 2018-11-14 17:22:31 -05:00
Ronald E. Miller a4835fa7a6 Merge branch 'master' of https://github.com/ProfessorMiller/lammps 2018-11-14 09:42:32 -05:00
julient31 d66a1ac054 Commit JT 111318 
- corrections pair/spin/dipolar/long
 2018-11-13 17:03:32 -07:00
Axel Kohlmeyer d1ff90eacf copy and rename fix_nh.cpp/.h to USER-CAUCHY/fix_cauchy.cpp/.h related changes 
this moves the code into the corresponding folders, renames the classes, adds copies of the doc files, moves the examples, integrates the USER-CAUCHY package into the build system.
 2018-11-13 17:18:37 -05:00
Steve Plimpton 5062c43aea rename example outputs 2018-11-12 12:32:53 -07:00
Steve Plimpton 3b7ebbb8df new hyper examples 2018-11-12 12:32:53 -07:00
Steve Plimpton d7a479d2f6 hyper example dir 2018-11-12 12:32:52 -07:00
julient31 9727fdc473 Commit JT 110818 
- correct bug (match ewald/disp results for vir)
- started correct mag. part
 2018-11-08 16:17:43 -07:00
Axel Kohlmeyer e0955f6434 Merge branch 'master' into sdpd to resolve merge conflicts 
# Conflicts:
#	cmake/CMakeLists.txt
#	src/Makefile
 2018-11-08 16:32:02 -05:00
Axel Kohlmeyer a6e9b99295
Merge pull request #1180 from gtribello/master 
Add natively supported PLUMED interface to LAMMPS
 2018-11-08 16:16:50 -05:00
jrgissing a37d718ed1 update bond/react examples 2018-11-03 12:01:00 -06:00
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 cf91a93876 update example to check if the store fix is removed properly 2018-10-23 10:41:51 -04:00
Axel Kohlmeyer baea04b913 update cauchystat example to conform more with standard LAMMPS examples 2018-10-23 10:41:51 -04:00
Axel Kohlmeyer c094831617 tweak example input and readme 2018-10-23 10:41:51 -04:00
Ronald E. Miller 5c686be33d clean up whitespace, indentation, isolate all cauchystat-related code, remove extraneous examples 2018-10-23 10:41:50 -04:00
Ronald E. Miller 43f83abe5e Changes to the NH fix enabling Cauchy stress control (Cauhchystat) due to Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 
144, 184107 (2016).
 2018-10-23 10:41:50 -04:00
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
julient31 a745a0aed0 Commit JT 100318 
- correction forces ewald_dipole
- correction mag. dipolar energy
 2018-10-03 10:23:58 -06:00
Ryan S. Elliott f61f43a56b Merge branch 'master' into kim-v2-update 2018-10-01 21:17:26 -05:00
julient31 19aaf294e5 Commit JT 092718 
- renamed pair/spin/long functions
- started to work on debugging ewald_dipole (force errors)
 2018-09-27 10:46:52 -06:00
Steve Plimpton 5a6226caa5 jive src headers with doc page entries and example scripts 2018-09-25 10:50:43 -06:00
julient31 6b4303c405 Commit2 JT 092418 
- initialized g_ewald before Newton solver
- mu2 is now adim in ewald_dipole_spin
 2018-09-24 16:40:59 -06:00
julient31 53a779067e Commit JT 092418 
- ewald_dipole_spin added
- accuracy problem (with eval of gewald and Newton solver)
 2018-09-24 10:59:17 -06:00
Ronald E. Miller 4b988b8cdf clean up whitespace, indentation, isolate all cauchystat-related code, remove extraneous examples 2018-09-24 11:30:06 -04:00
julient31 cce9fe4a34 Commit2 JT 092118 
- created pair_spin_dipolar_cut
- real-space short-range calc of the spin dipolar interaction
- run and check valgrind ok
 2018-09-21 09:55:41 -06:00
julient31 82a5346ab1 Commit JT 091418 
- created pair_spin_long_qsymp
- modified ewald_dipole
 2018-09-14 15:09:59 -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
Ronald E. Miller f120b18db8 Changes to the NH fix enabling Cauchy stress control (Cauhchystat) due to Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 
144, 184107 (2016).
 2018-09-04 15:28:57 -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
julient31 16911adcea Commit1 JT 083018 
- started to work on ewald_dipole (not yet triclinic)
- compiles and runs (no memory issue)
- check the energy accuracy
 2018-08-30 07:33:25 -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
julient31 cf1d421e10 Commit JT 082318 
- corrected memory errors in pppm_dipole and pppm_dipole_spin
- created fm_long in atom_vec_spin
- fm_long added to fm in initial_integrate (in ComputeInteractionsSpin)
 2018-08-23 15:18:30 -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