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1643 Commits

Author SHA1 Message Date
Yury Lysogorskiy
d29ae7af92 upd ML-PACE.cmake and Install.py (new version v.2023.10.04 and checksum) that should fix build issues with KOKOKOS 2023-10-13 12:05:28 +02:00
Yury Lysogorskiy
0536e0e7b3 upd Install.py (new version v.2023.10.04.pre and checksum) 2023-10-04 12:38:25 +02:00
Axel Kohlmeyer
c3cc4974d1 silence uninitialized access valgrind warning 2023-09-21 07:33:03 -04:00
Axel Kohlmeyer
822ad5b866 change refereces to lib/smd and smd to lib/machdyn and machdyn 2023-09-13 15:51:41 -04:00
Axel Kohlmeyer
dd18de164a avoid legacy compilation failures on recent ubuntu machines that only have python3-config 2023-08-12 12:41:44 -04:00
Axel Kohlmeyer
2f415c8b62 bugfix for pair style dpd/gpu from Trung 2023-08-09 09:42:01 -04:00
Axel Kohlmeyer
0446bdfc00 work around C++17 issue in AWPMD package 2023-08-03 21:56:04 -04:00
Axel Kohlmeyer
794e3d11df Merge pull request #3670 from stanmoore1/kk_update_4.0 
Update Kokkos library in LAMMPS to v4.1.0
 2023-08-03 17:36:22 -04:00
Axel Kohlmeyer
6e9a6e6b0b Merge pull request #3856 from akohlmey/remove-mscg-package 
Remove MSCG package from LAMMPS distribution
 2023-08-03 17:29:56 -04:00
Stan Gerald Moore
e0055ea929 Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0 2023-08-03 13:42:48 -06:00
Axel Kohlmeyer
021eeae860 add workaround for failing overhead estimation test on (Intel) GPUs that only support single precision 2023-07-18 13:24:11 -04:00
Axel Kohlmeyer
74c5ca0996 move definition of struct containing double to avoid failure on Intel Xe GPU 2023-07-17 18:34:03 -04:00
Axel Kohlmeyer
fa4a3a0622 using NBOR_PREFETCH=2 gives errors with Intel Xe GPUs set to 0 2023-07-17 18:33:21 -04:00
Axel Kohlmeyer
d27ab47ed9 for clarity 2023-07-17 18:32:18 -04:00
Axel Kohlmeyer
9b7bd71ab6 remove MSCG package from LAMMPS distribution 2023-07-16 21:04:58 -04:00
Stan Gerald Moore
78470febbd Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0 2023-07-14 17:59:15 -06:00
Axel Kohlmeyer
be2e437cec use approximation for erfc() on OpenCL for Intel since the OpenCL version seems broken 2023-07-14 10:08:59 -04:00
Axel Kohlmeyer
620c60122a should not use pow() for computing cube, use multiplication. 2023-07-14 10:08:09 -04:00
Trung Nguyen
d6412dc97b Attempted to resolve issues with switching from acctyp4 to acctyp3 in tep, fieldp since the changes in PR #3675, noting some changes with Intel OCL PR #3663 2023-07-08 00:50:19 -05:00
Stan Gerald Moore
3c09aa26f9 Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0 2023-07-03 16:35:57 -06:00
Stan Gerald Moore
330107b77b Update Kokkos library in LAMMPS to v4.1.0 2023-06-29 10:42:42 -06:00
Axel Kohlmeyer
e95b10f24a update VMD plugin headers to the latest version 2023-06-21 06:44:09 -04:00
ilia-nikiforov-umn
6f5e5746b3 Update lib/kim/README 
Fix some typos and update to non-deprecated form of kim commands
 2023-06-16 12:21:42 -05:00
Stan Gerald Moore
0564d79570 Fix SYCL compile error with GNU make, see https://github.com/kokkos/kokkos/pull/6218 2023-06-14 10:52:47 -06:00
Axel Kohlmeyer
f128de7dd0 Bugfix from @ndtrung81 for indexing bug when tallying per-atom Coulomb energy 2023-06-13 15:13:16 -04:00
Stan Gerald Moore
8ddd965127 Update Kokkos library in LAMMPS to v4.0.1 2023-06-05 15:03:28 -06:00
Stan Gerald Moore
741db3da28 Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0 2023-06-05 10:55:24 -06:00
Stan Gerald Moore
966efd8bd5 Add missed changes 2023-06-05 10:33:30 -06:00
Stan Gerald Moore
a12133ce03 Update Kokkos library in LAMMPS to v3.7.2 2023-06-05 09:59:38 -06:00
Giacomo Fiorin
377c652a83 Update Colvars library to version 2023-05-01 
This update consists exclusively of bugfixes or maintenance-related changes.

The following is a list of pull requests in the Colvars repository since the previous update to LAMMPS:

- 532 Add XYZ trajectory reading feature
  https://github.com/Colvars/colvars/pull/532 (@jhenin, @giacomofiorin)

- 531 Delete objects quietly, unless explicitly requested via script (including VMD)
  https://github.com/Colvars/colvars/pull/531 (@giacomofiorin)

- 530 Append newline to log and error messages if not already present
  https://github.com/Colvars/colvars/pull/530 (@giacomofiorin)

- 528 Forward-declare OpenMP lock
  https://github.com/Colvars/colvars/pull/528 (@giacomofiorin)

- 527 Remove unneeded STL container
  https://github.com/Colvars/colvars/pull/527 (@giacomofiorin)

- 526 Allow collecting configuration files and strings before setting up interface
  https://github.com/Colvars/colvars/pull/526 (@giacomofiorin, @jhenin)

- 523 Fallback to linearCombination when customFunction is missing in customColvar
  https://github.com/Colvars/colvars/pull/523 (@HanatoK, @giacomofiorin)

- 522 Use iostream::fail() to check for I/O error
  https://github.com/Colvars/colvars/pull/522 (@jhenin)

- 520 Fix ref count
  https://github.com/Colvars/colvars/pull/520 (@giacomofiorin)

- 513 Set target temperature through a common code path
  https://github.com/Colvars/colvars/pull/513 (@giacomofiorin, @jhenin)

- 509 Safer detection of Windows with recent Microsoft Visual Studio versions
  https://github.com/Colvars/colvars/pull/509 (@akohlmey)

- 508 Update LAMMPS patching method to reflect Lepton availability
  https://github.com/Colvars/colvars/pull/508 (@giacomofiorin)

- 497 Increase the precision of write_multicol
  https://github.com/Colvars/colvars/pull/497 (@HanatoK)

- 496 Only perform MTS automatic enable/disable for timeStepFactor > 1
  https://github.com/Colvars/colvars/pull/496 (@giacomofiorin)

- 493 Remove unused branch of quaternion input function
  https://github.com/Colvars/colvars/pull/493 (@giacomofiorin)

- 489 Ensure there are spaces between the fields in the header
  https://github.com/Colvars/colvars/pull/489 (@HanatoK)

- 487 Use map of output streams, and return references to its elements
  https://github.com/Colvars/colvars/pull/487 (@giacomofiorin, @jhenin)

- 486 Remember first step of moving restraint
  https://github.com/Colvars/colvars/pull/486 (@jhenin)

- 485 Add decoupling option for moving restraints
  https://github.com/Colvars/colvars/pull/485 (@jhenin)

- 483 Update Lepton via patching procedure
  https://github.com/Colvars/colvars/pull/483 (@giacomofiorin)

- 481 Make file-reading operations of input data abstractable
  https://github.com/Colvars/colvars/pull/481 (@giacomofiorin)

Authors: @akohlmey, @giacomofiorin, @HanatoK, @jhenin
 2023-05-17 13:29:00 -04:00
Stan Moore
0be9206c08 Merge branch 'develop' into kk_update_4.0 2023-04-24 09:05:29 -06:00
Axel Kohlmeyer
b9c940926f silence compiler warnings 2023-04-22 17:50:41 -04:00
Axel Kohlmeyer
c6c470a2c9 compilation fix for Fedora 38 from upstream 2023-04-22 13:04:47 -04:00
Stan Gerald Moore
f138117ecf Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0 2023-04-18 12:36:08 -06:00
Stan Gerald Moore
f2e1bf5116 Merge branch 'kk_update_4.0' of github.com:stanmoore1/lammps into kk_update_4.0 2023-04-18 12:35:51 -06:00
Stan Gerald Moore
5a25d5310b Fix bug in Makefile.kokkos 2023-04-18 12:35:30 -06:00
Axel Kohlmeyer
fbded8d8f4 include fix from @ndtrung81 2023-04-13 20:06:35 -04:00
Axel Kohlmeyer
c68e71a24f update Purge.list and .gitignores 2023-03-29 17:33:58 -04:00
Steve Plimpton
44fc1c55f6 Merge branch 'develop' into remove-fix-latte 2023-03-29 14:43:45 -06:00
Stan Gerald Moore
1991332887 Merge branch 'develop' of github.com:lammps/lammps into kk_update_4.0 2023-03-24 09:17:32 -06:00
Axel Kohlmeyer
ed8b06a756 Merge pull request #3628 from lammps/fix-mdi-qmmm 
Add a fix mdi/qmmm command for running QMMM via MDI code coupling
 2023-03-23 12:33:00 -04:00
Axel Kohlmeyer
08153b7b4d trim list of known plumed source packages. 2023-03-16 21:01:32 -04:00
Axel Kohlmeyer
d8d1235773 update MDI library version to 1.4.16 2023-03-14 11:59:19 -04:00
Axel Kohlmeyer
0e2b2eb266 Merge branch 'develop' into collected-small-changes 2023-03-13 22:47:08 -04:00
Axel Kohlmeyer
92302d0f22 Merge branch 'develop' into mar2023_gpu_misc 2023-03-13 19:02:20 -04:00
Axel Kohlmeyer
21293f1c08 update links and hashes for new plumed2 releases 2023-03-13 12:10:41 -04:00
Axel Kohlmeyer
1887495434 Merge branch 'develop' into fix-mdi-qmmm 2023-03-12 00:53:40 -05:00
W. Michael Brown
c96ac858bf GPU Package: Adding JIT test for OpenCL prefetch support. 2023-03-07 21:43:19 -08:00
Axel Kohlmeyer
68ed9ec85e Merge branch 'develop' into collected-small-changes 2023-03-07 19:39:26 -05:00
W. Michael Brown
d7c783560a GPU Package: Fixing out of bounds memory access issues with special kernel unroll optimizations. 2023-03-06 22:11:10 -08:00