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954 Commits

Author SHA1 Message Date
Axel Kohlmeyer 77a38c2a0a
remove (unsupported) reference to AMD Ryzen 2020-06-11 17:03:20 -04:00
Axel Kohlmeyer 64a4e5e21a
make kokkos configuration keywords in traditional build case insensitive 2020-06-10 15:53:09 -04:00
Axel Kohlmeyer 9bf47cd9f3
make KOKKOS library compilation compatible with mode=shared 2020-06-05 13:58:11 -04:00
Axel Kohlmeyer 3b77546eb9
Merge pull request #2069 from junghans/latte_v1.2.2 
latte: bump to v1.2.2
 2020-05-07 14:27:19 -04:00
Christoph Junghans 69a6a8e064 pull in kokkos-3.1.01 2020-05-07 10:22:42 -06:00
Christoph Junghans fe62e1dbc9 latte: bump to v1.2.2 2020-05-05 10:51:11 -06:00
Axel Kohlmeyer fdb4ba51da
add patch to VORONOI package external build so it will compile with BSD make 2020-05-03 04:04:02 -04:00
Axel Kohlmeyer e8d4cc424e
use different header for alloca(3) on *BSD 2020-05-03 01:10:04 -04:00
Axel Kohlmeyer 74e8505a1f
Merge branch 'master' into collected-small-changes 2020-04-27 16:57:47 -04:00
Axel Kohlmeyer 121b40ebaa
Merge pull request #2026 from ndtrung81/ellipsoid-gpu-special-bonds 
Fixed bugs with special bonds for ellipsoid gpu pair styles
 2020-04-27 16:15:58 -04:00
Axel Kohlmeyer 0a9bed0ca6
Merge branch 'cmake_clean_up_plumed' of github.com:junghans/lammps into collected-small-changes 2020-04-27 16:07:52 -04:00
Yaser Afshar 437967bfd8 adding the standard header to prevent ‘NULL’ was not declared error 2020-04-27 12:49:03 -05:00
Axel Kohlmeyer f1aaad2b13
remove trailing whitespace 2020-04-27 09:54:05 -04:00
Axel Kohlmeyer d53e468ce0
do not mix c++ style and c-style comments 2020-04-26 22:50:24 -04:00
Axel Kohlmeyer 0b6e5be379
cosmetic edit to trigger new CI test runs 2020-04-26 00:25:07 -04:00
Christoph Junghans 7fd50045fe USER-PLUMED: remove unused defines 2020-04-25 10:16:58 -06:00
Trung Nguyen 1295a9ef46 Fixed bugs with special bonds for ellipsoid gpu pair styles 2020-04-25 10:28:18 -05:00
Stan Moore ba8d043c7e Update Kokkos library in LAMMPS to v3.1 2020-04-16 09:06:08 -06:00
Giacomo Fiorin be1f307384 Add defines to build Lepton with MSVC and traditional make 2020-04-14 16:57:04 -04:00
Axel Kohlmeyer 209a3fde71
use MY_PI everywhere, not M_PI. 2020-04-13 12:02:53 -04:00
Axel Kohlmeyer 5d2ec73c5d
re-enable cross-compilation with mingw64 2020-04-13 11:22:19 -04:00
Richard Berger 0608002451 Remove trailing whitespace 2020-04-10 15:10:41 -04:00
Richard Berger 438ee4d75b Merge remote-tracking branch 'origin/master' into gpu_hip 2020-04-08 13:49:41 -04:00
Stan Moore 72200a9958 Fix MPI environment variable issue in Makefile.kokkos 2020-04-01 08:57:18 -06:00
Richard Berger 19a52dc506 Update lib/gpu/.gitignore 2020-03-30 17:36:22 -04:00
Richard Berger 373b57cfdc Change 'echo -e' to 'printf' for greater compatibility 2020-03-30 17:36:00 -04:00
Richard Berger 4f6dd381c3 Merge branch 'master' into gpu_hip 2020-03-30 17:15:55 -04:00
Stan Moore 50935b5cbc Fix typos 2020-03-25 14:23:45 -06:00
Stan Moore 60864e38d1 Update Kokkos library in LAMMPS to v3.0 2020-03-25 14:08:39 -06:00
Axel Kohlmeyer 7f53cbc1a0
fix grammar issue 2020-03-17 20:33:37 -04:00
Axel Kohlmeyer e000c46c8c
correct spelling 2020-03-17 20:29:18 -04:00
Eisuke Kawashima 649a8cc01a
Fix typo 2020-03-14 13:57:48 +09:00
Eisuke Kawashima 8af9d40392
Update DOI resolver 
https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
 2020-03-12 16:53:24 +09:00
Axel Kohlmeyer 1fb54c307c
Merge pull request #1918 from akohlmey/collected-small-fixes 
Collected small fixes for the next patch
 2020-03-05 15:16:50 -05:00
Axel Kohlmeyer 5a3a5d86d4
reduce compiler warnings and avoid clash with KOKKOS 2020-03-05 14:27:33 -05:00
Axel Kohlmeyer fb3a8f5bb1
Merge pull request #1909 from giacomofiorin/colvars-update 
Update Colvars to version 2020-02-27
 2020-03-05 10:18:01 -05:00
Miguel Dias Costa 8765b14377 add EPYC to KOKKOS_ARCH_LIST 2020-03-01 13:45:06 +08:00
Giacomo Fiorin 7be004512f Update Colvars to version 2020-02-27 
This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
 2020-02-27 19:55:31 -05:00
Axel Kohlmeyer 0db0d5408a
update instructions for in qmmm README to cover both build systems and include more details 2020-02-20 16:59:06 +01:00
Axel Kohlmeyer 8a52e5dbe7
fix logic error in generic Install.py script when a Makefile.lammps is missing 2020-02-19 18:10:32 +01:00
mariella ippolito cc3a7c37cb more lib compilation updates 2020-02-18 11:16:08 +01:00
mariella ippolito 36458a95b7 Updated 2020-02-18 10:59:51 +01:00
mariella ippolito 387a283157 more lib compilation updates 2020-02-18 10:55:13 +01:00
mariella ippolito 82b57bd3b8 Upfated Makefile.foo inside lib/qmmm 2020-02-18 10:47:04 +01:00
Axel Kohlmeyer 4cacc4701d
update plumed support to include version 2.6.0. Fix bug in API check 2020-02-13 16:03:58 +01:00
Vsevak d024b3d340 Add shared memory optimization 2020-02-12 01:35:44 +03:00
Vsevak 33fc22b752 Fix echo in Makefile 2020-02-03 01:55:20 +03:00
Vsevak 9e8806bd22 Addition to lib/gpu/README for HIP 2020-01-31 21:26:52 +03:00
Giacomo Fiorin 9427fc50a5 Update Colvars library to version 2020-01-27 
One new feature (arithmetic path variables) and several smaller enhancements
or bugfixes.

    Fix error check when loading an old state file
    https://github.com/Colvars/colvars/pull/317

    Get default values for grid boundaries when available
    https://github.com/Colvars/colvars/pull/310

    Allow redefining existing index groups (warn when this happens)
    https://github.com/Colvars/colvars/pull/302

    Simplified replica communication syntax in metadynamics
    https://github.com/Colvars/colvars/pull/301

    Obtain the bias_energy for ABF biases
    https://github.com/Colvars/colvars/pull/294

    Fix reading path file with vector CVCs
    https://github.com/Colvars/colvars/pull/288

    Fix segfault at deleting CVBasedPath
    https://github.com/Colvars/colvars/pull/286

    Parrinello's (arithmetic) pathCV in CV space
    https://github.com/Colvars/colvars/pull/274

    Fix race condition when starting a bundle of walkers
    https://github.com/Colvars/colvars/pull/279
 2020-01-28 14:15:05 -05:00
Vsevak 66c5fa2abd Merge 'gpu_hip_port' into master 2020-01-28 20:35:08 +03:00