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918 Commits

Author SHA1 Message Date
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
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 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
Axel Kohlmeyer 18a0cd3ead
Merge pull request #1817 from akohlmey/collected-small-fixes 
Collected small bugfixes and updates
 2020-01-08 17:16:34 -05:00
Axel Kohlmeyer d3eed9dba4
Merge pull request #1752 from ndtrung81/gpu-mem-leak-init 
Fixed bugs with kernel (re)compiling when the global device got clear and reinitialized
 2020-01-08 16:17:13 -05:00
Axel Kohlmeyer 6e2c3b7ce9
Merge branch 'master' into collected-small-fixes 2020-01-08 16:14:19 -05:00
Axel Kohlmeyer 481c647889
Merge pull request #1776 from Vsevak/tip4p_gpu 
GPU support for lj/cut/tip4p/long pair style
 2020-01-08 15:35:39 -05:00
Axel Kohlmeyer 00dce6b198
Merge branch 'master' into gpu-mem-leak-init 2020-01-08 14:26:03 -05:00
Vsevak e8a941a0b9 Remove unnecessary data transfer from tip4p/gpu pairstyle init 
Such data transfer is performed at each timestep, so it does not belong to the initialization
 2020-01-08 01:48:47 +03:00
Axel Kohlmeyer 66a473455e
silence warnings from generic OpenCL header files (as seen on Fedora 31) 2020-01-06 17:34:26 -05:00
Vsevak 337b0fd649 Fix 'sametag' transfer 2019-12-22 20:20:12 +03:00
Trung Nguyen 4c3ec145f3 Corrected the wrong use of the stubs path in -rpath 2019-12-17 14:05:39 -06:00
Trung Nguyen 7e8a04d985 More minor update to README 2019-12-12 09:57:49 -06:00
Trung Nguyen 99ba15bf6a Updated README and added -L$(CUDA_HOME)/lib64/stubs to the Makefile's 2019-12-11 16:29:42 -06:00
Vsevak a3fca53e97 Separate the computation of newsite into another kernel 
This eliminates the need for thread fence and makes the calculation stable on GTX1070 (CUDA and OpenCL) and TitanV
 2019-12-07 15:54:20 +03:00
Vsevak 4a51e1660f Add thread fence in kernel to fix Volta indeterminacy 2019-12-07 01:16:39 +03:00
Vsevak a2f9fa8e78 Separate the computation of hneigh into another kernel 
Simplify the main GPU kernel and add another kernel 'k_pair_reneigh'. It works good on GTX1070 (Pascal), but still there is a problem with non-deterministic results on Volta.

I reimplement BaseCharge::compute methods in the child class LJ_TIP4PLong to correctly embed a new kernel in the code.

Also commit includes some codestyle fixes.
 2019-12-06 21:41:02 +03:00
Vsevak 66a076b819 Delete "float.h" from TIP4P GPU kernel for better OpenCL compatibility 
According to Khronos OpenCL docs, "The C99 standard headers <...>, float.h, <...> are not available and cannot be included by a program"
 2019-11-27 19:49:12 +03:00
Vsevak 4febc7f794 Add copyright and fix style 2019-11-18 02:01:32 +03:00
Vsevak ca8d1ac2ff Simplify tip4p GPU memory resize using 'resize_ib' 2019-11-18 02:01:32 +03:00
Vsevak f803ba5655 Add shfl_xor sum to kernel for ARCH>=300 2019-11-12 21:35:36 +03:00
Vsevak 64bdc59623 Implement GPU pair style lj/cut/tip4p/long/gpu 
Source code, Makefiles and Install for GPU-accelerated TIP4P pair style.
It is implemented as a part of the standard GPU package.
The style is compatible with the standard  lj/cut/tip4p/long.
Also, this commit modifies "atom.h" just to
add a getter for variable 'max_same'.
 2019-11-10 02:38:58 +03:00
Trung Nguyen e119bffcca Fixed bugs with kernel (re)compiling when the global device got cleared and then reinitialized 2019-10-31 01:15:53 -05:00
Michael Brown a0d74ca2ae Bug fix for gay-berne potential when mu != 1.0. 2019-10-27 22:31:00 -07:00
Axel Kohlmeyer b631362137
Merge pull request #1735 from ndtrung81/gpu-mem-leak-init 
Gpu mem leak with init invoked multiple times
 2019-10-25 17:08:21 -04:00
Axel Kohlmeyer e7cb2f4cac
put back overly eager deleted code that is used without -DNDEBUG 2019-10-21 03:25:21 -04:00
Axel Kohlmeyer 08b55c4ca5
silence compiler warning 2019-10-20 19:00:54 -04:00
Axel Kohlmeyer c144b1af71
fix typos 2019-10-20 18:42:22 -04:00
Axel Kohlmeyer 6767fa5604
update supported plumed library to version 2.5.3 2019-10-20 16:27:32 -04:00
Axel Kohlmeyer 67512f8afc
remove bogus POEMS header files from AtC lib folder 2019-10-20 16:13:03 -04:00
Axel Kohlmeyer b705525734
resolve unused parameter warnings in USER-ATC package 2019-10-20 13:36:06 -04:00
Trung Nguyen 86f644979c Updated pppm 2019-10-20 00:18:28 -05:00
Trung Nguyen dfbee32575 Fixing issues with growing memory allocation with multiple init calls 2019-10-19 23:35:52 -05:00
Axel Kohlmeyer f4fcd2a911
flag that MESSAGE package is not compatible with -DLAMMPS_BIGBIG 2019-10-19 09:50:07 -04:00
Axel Kohlmeyer d684b70555
reduce compiler warnings in USER-AWPMD 2019-10-18 15:57:07 +02:00
Giacomo Fiorin 693e34b587 Print parsed compiler flags, some cosmetic changes for added consistency 2019-10-17 22:53:13 -04:00