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1024 Commits

Author SHA1 Message Date
Axel Kohlmeyer 28812b1ea7
Merge pull request #2381 from akohlmey/collected-small-changes 
Collected small changes
 2020-09-24 16:17:28 -04:00
Axel Kohlmeyer 9df1bb4db0
remove obsolete makefiles. Makefile.xk7 is on death watch but Blue Waters still has such nodes 2020-09-22 17:47:14 -04:00
Vsevak 459d51bbea Do not disable atomics for HIP 
atomics are disabled for NVIDIA 1.0 cards, which should not affect ROCm HIP
 2020-09-22 22:34:24 +03:00
Axel Kohlmeyer 7b4304577a
add -std=c++11 flag to compilation of all .cpp files on Linux 2020-09-22 10:58:54 -04:00
Axel Kohlmeyer 2d7b6a9008
remove dead code 2020-09-22 10:12:59 -04:00
Giacomo Fiorin 7deb773440 Update Colvars to version 2020-09-17 
Small changes

Implement global map of components (@HanatoK)
https://github.com/Colvars/colvars/pull/363

Format code examples with colored background (@giacomofiorin)
https://github.com/Colvars/colvars/pull/361

replaced jacobi() with an open-source version (@jewettaij)
https://github.com/Colvars/colvars/pull/360
 2020-09-18 17:09:18 -04:00
Axel Kohlmeyer 4e304177a1
Merge pull request #2356 from giacomofiorin/colvars-update 
Update Colvars to version 2020-07-07
 2020-09-16 23:37:02 -04:00
Anne Gunn 6315b277c8 Revert commit 14dfd3876a which walked-back 
the NULL->nullptr changes for lib/awpmd.

Then, hand-applied a minor cleanup to comments, ala Axel's changes to the
rest of the codebase.
 2020-09-14 12:05:46 -06:00
Anne Gunn 430d151660 Revert commit 05d41cd50d which walked-back 
the NULL->nullptr changes for lib/poems.

Then, hand-applied a minor cleanup to comments, ala Axel's changes to the
rest of the codebase.
 2020-09-14 12:05:46 -06:00
Axel Kohlmeyer ec1fe4e445 update molfile plugin headers with latest versions from VMD 2020-09-14 12:05:45 -06:00
Anne Gunn 96b01f2383 T2345: Walking back nullptr changes to lib/awpmd 2020-09-14 12:05:45 -06:00
Anne Gunn ed57554e18 T2345: Replace instances of NULL with nullptr 
revert lib/poems to remove nullptr changes.
Walking back changes to lib as needed.
 2020-09-14 12:05:44 -06:00
Anne Gunn f524fa758d T2345: Replace instances of NULL with nullptr 
Per guidance from Axel, revert lib/kokkos and lib/colvars
to remove nullptr changes.
 2020-09-14 12:05:44 -06:00
Anne Gunn 9a5d8fd18b Manually resolve two rebase conflicts. 2020-09-14 12:04:51 -06:00
Giacomo Fiorin 85c394453c Update Colvars to version 2020-07-07 
This update contains several fixes and small new features or usability
improvements.  Descriptions and authorship information can be accessed from
the pull requests listed below.

Skip the zero-step also when multiple run commands are executed in sequence (@giacomofiorin)
https://github.com/Colvars/colvars/pull/357

Do not accumulate data at step 0 (@giacomofiorin)
https://github.com/Colvars/colvars/pull/345

Support for symmetry permutations of atoms in RMSD (@jhenin)
https://github.com/Colvars/colvars/pull/344

Detect new grid parameters (@jhenin)
https://github.com/Colvars/colvars/pull/341

Only access the output streams in non-threaded regions (@giacomofiorin)
https://github.com/Colvars/colvars/pull/338

Fix incomplete setting of default colvarsRestartFrequency (@giacomofiorin)
https://github.com/Colvars/colvars/pull/334

Fix typo (@e-kwsm)
https://github.com/Colvars/colvars/pull/333

Convert the input keyword to lowercase in read_state_data_key (@HanatoK)
https://github.com/Colvars/colvars/pull/332

Implement reflecting b.c. for ext Lagrangian (@jhenin)
https://github.com/Colvars/colvars/pull/329
 2020-09-09 18:19:21 -04:00
Axel Kohlmeyer 9afba50d01
update for zstd support 2020-09-07 21:00:45 -04:00
Axel Kohlmeyer ceed9284c1
Merge branch 'master' into collected-small-changes 2020-09-04 13:32:47 -04:00
Axel Kohlmeyer 90c13b1b14
update build files for plumed 2.6.1 release 2020-09-04 11:44:39 -04:00
Axel Kohlmeyer 203e42073a
fix compilation error 2020-09-02 22:51:14 -04:00
Axel Kohlmeyer d5027c125c
rename fmt() macro to logfmt() to avoid clashes with fmtlib 2020-09-02 17:58:22 -04:00
Axel Kohlmeyer 67a5db03c7
Merge pull request #2326 from ndtrung81/gpu-update-makefiles 
update makefiles in lib/gpu for more recent architectures
 2020-08-31 12:30:28 -04:00
Trung Nguyen ecb1f266b5 More updates 2020-08-30 15:10:29 -05:00
Trung Nguyen 7a5f193c02 Updated several Makefile's in lib/gpu for newer compute capabilities 2020-08-30 15:06:44 -05:00
Axel Kohlmeyer fdb726629f
revert "fix" for pair style beck/gpu and correct beck and beck/omp instead 
we should consistently apply factor_lj for both, force and energy, or not
 2020-08-27 17:14:05 -04:00
Axel Kohlmeyer a4f1be8fe3
Merge branch 'master' into gpu-bugfix 2020-08-27 17:05:26 -04:00
Trung Nguyen e4e15157f8 Fixed bugs in the GPU kernels of pair styles beck/gpu and gauss/gpu involving factor_lj 2020-08-26 23:41:00 -05:00
Axel Kohlmeyer d00807ee9a
Merge pull request #2311 from stanmoore1/kk_update_3.2 
Update Kokkos library in LAMMPS to v3.2
 2020-08-26 15:35:25 -04:00
Stan Moore 4d90c2b74b Update Kokkos library in LAMMPS to v3.2 2020-08-25 20:21:48 -06:00
Vsevak 0842911cd8 Rename local buffers 'red_acc' in lal_tersoff* 
Rename __local red_acc in lal_tersoff
 2020-08-23 22:22:28 +03:00
Axel Kohlmeyer 8e74d5ad02
Eigen3 is now hosted at GitLab. The bitbucket repo is gone. Update URLs and MD5s 2020-08-18 21:29:43 -04:00
Axel Kohlmeyer 7e5e741ea1
update code for ufm/gpu to match changes in base class where uf4 is removed 2020-08-03 08:12:09 -04:00
Vsevak db47eeb2a9 Fix handling of CL_DEVICE_TYPE flags 2020-07-31 19:21:32 +03:00
Axel Kohlmeyer 29c50671da
Merge pull request #2254 from Vsevak/fix_opencl 
Fix corrupted character in GPU package
 2020-07-27 20:08:18 -04:00
Axel Kohlmeyer 477b97f257
remove some more extended ASCII characters 2020-07-27 17:33:35 -04:00
Axel Kohlmeyer 2bb5c53a47
remove/replace extended ASCII characters from comments 2020-07-27 17:15:29 -04:00
Axel Kohlmeyer 634f274a04
whitespace cleanup: replace tabs and remove trailing whitespace 2020-07-27 17:14:53 -04:00
Vsevak 93f14e9bba Fix broken ASCII symbol in GPU package 2020-07-27 20:16:55 +03:00
Trung Nguyen ebfe7f68af More cleanup 2020-07-05 00:20:28 -05:00
Trung Nguyen c488e6208d Similar bug fixes to vashishta/gpu 2020-07-04 23:52:32 -05:00
Trung Nguyen adacc7f2a4 Similar bug fixes for tersoff/mod/gpu and tersoff/zbl/gpu; some cleanup for sw/gpu 2020-07-04 19:08:55 -05:00
Trung Nguyen 9f733fb305 Removed unused variables 2020-07-04 00:23:34 -05:00
Trung Nguyen 6de020805f Fixed a bug with tersoff/gpu with building the short neighbor list 2020-07-03 23:55:26 -05:00
Axel Kohlmeyer 66271448ae
Merge pull request #2167 from Vsevak/master 
Update GPU CMake and Makefile scripts for ROCm v3.5
 2020-06-26 13:43:32 -04:00
Axel Kohlmeyer 3c19a49605
Merge pull request #2190 from akohlmey/more-fmtlib-uses 
Reduce use of local print buffers, simplify output handling with std::string and fmtlib
 2020-06-26 12:08:46 -04:00
Axel Kohlmeyer d46a1254e4
remove non-ASCII characters. 2020-06-25 21:11:32 -04:00
Vsevak 496bd55dc9 Fix lj/cut/tip4p/long/gpu virial 2020-06-25 17:30:51 +03:00
Vsevak 0ba701acd7 Remove trailing space 2020-06-20 17:25:16 +03:00
Vsevak 723b9e6760 Try to keep compatibility with deprecated ROCm hcc compiler 2020-06-20 15:17:54 +03:00
Vsevak 8eed1b27ff GPU Makefile cleanup 2020-06-19 00:07:10 +03:00
Vsevak f75b8e1688 Fix Makefile for GPU ROCm 3.5 backend 2020-06-18 00:33:46 +03:00