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905 Commits

Author SHA1 Message Date
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
Giacomo Fiorin c578e4e7fc Enable COLVARS_LEPTON for make, update build doc for USER-COLVARS 2019-10-17 22:48:57 -04:00
Giacomo Fiorin b6af3c7ad0 Conventional make tweaks to handle Lepton C++11 requirement 2019-10-14 16:05:45 -04:00
Giacomo Fiorin e04a18fc4f Upgrade Lepton library to version 2019-06-02 2019-10-14 16:05:45 -04:00
Axel Kohlmeyer b72215fe02
add support for automated checksumming of downloaded sources to kim api conventional build 2019-08-16 12:43:37 -04:00
Ryan S. Elliott 42711245a2 bump kim-api to 2.1.3 2019-08-16 10:08:23 -06:00
Axel Kohlmeyer 16bf916dd0
Merge pull request #1616 from akohlmey/fixes-for-stable 
Collected small fixes for stable release
 2019-08-05 16:48:50 -04:00
Giacomo Fiorin 97501f0946 Fix typo 2019-08-05 14:59:40 -04:00
Giacomo Fiorin 51ba9bd520 Bugfix for Colvars library (update to version 2019-08-05) 
Bugfix for group2CenterOnly (coordNum option):
https://github.com/Colvars/colvars/pull/278
 2019-08-05 14:14:33 -04:00
Axel Kohlmeyer 0774e92ece
use KIM-API 2.1.2 consistently with CMake and conventional build system 2019-08-03 06:40:31 -04:00
Axel Kohlmeyer 11198e9d29
Merge pull request #1607 from giacomofiorin/colvars-update 
Update Colvars to version 2019-08-01
 2019-08-02 10:43:13 -04:00
Giacomo Fiorin 52e2db44a1 Update Colvars to version 2019-08-01 
One new feature (geometric path variables) and bugfixes.

Minimize occurrence of file-read errors in multiple-walker metadynamics
https://github.com/Colvars/colvars/pull/276

Better error messages for RMSD
https://github.com/Colvars/colvars/pull/272

Ensemble-biased metadynamics documentation
https://github.com/Colvars/colvars/pull/261

Fix bug on multiple walkers metadynamics, pmf included twice
https://github.com/Colvars/colvars/pull/259

Implementation of the geometric path collective variables (C++11-only feature)
https://github.com/Colvars/colvars/pull/249
 2019-08-01 15:15:58 -04:00
Axel Kohlmeyer 2b288bc9e0
add missing mode keyword for substitution 2019-07-30 16:53:27 -04:00
Axel Kohlmeyer 882b2301bb
handle shared library extension on macosx for plumed runtime build 2019-07-30 16:48:50 -04:00