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1115 Commits

Author SHA1 Message Date
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
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
julient31 d66a1ac054 Commit JT 111318 
- corrections pair/spin/dipolar/long
 2018-11-13 17:03:32 -07:00
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 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
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
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