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951 Commits

Author SHA1 Message Date
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
Vsevak
43a9936241 Fix tagint usage 2020-01-20 03:38:58 +03:00
Vsevak
f69a17dd3a Reduce unnecessary data exchanges 2020-01-19 02:05:16 +03:00
Axel Kohlmeyer
514271c984 recover compilation with -DLAMMPS_BIGBIG and fix whitespace and formatting issues 2020-01-08 17:57:54 -05:00