7f53cbc1a0
fix grammar issue
2020-03-17 20:33:37 -04:00
e000c46c8c
correct spelling
2020-03-17 20:29:18 -04:00
649a8cc01a
Fix typo
2020-03-14 13:57:48 +09:00
8af9d40392
Update DOI resolver
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https://www.doi.org/doi_handbook/2_Numbering.html#htmlencoding
2020-03-12 16:53:24 +09:00
1fb54c307c
Merge pull request #1918 from akohlmey/collected-small-fixes
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Collected small fixes for the next patch
2020-03-05 15:16:50 -05:00
5a3a5d86d4
reduce compiler warnings and avoid clash with KOKKOS
2020-03-05 14:27:33 -05:00
fb3a8f5bb1
Merge pull request #1909 from giacomofiorin/colvars-update
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Update Colvars to version 2020-02-27
2020-03-05 10:18:01 -05:00
8765b14377
add EPYC to KOKKOS_ARCH_LIST
2020-03-01 13:45:06 +08:00
7be004512f
Update Colvars to version 2020-02-27
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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
0db0d5408a
update instructions for in qmmm README to cover both build systems and include more details
2020-02-20 16:59:06 +01:00
8a52e5dbe7
fix logic error in generic Install.py script when a Makefile.lammps is missing
2020-02-19 18:10:32 +01:00
cc3a7c37cb
more lib compilation updates
2020-02-18 11:16:08 +01:00
36458a95b7
Updated
2020-02-18 10:59:51 +01:00
387a283157
more lib compilation updates
2020-02-18 10:55:13 +01:00
82b57bd3b8
Upfated Makefile.foo inside lib/qmmm
2020-02-18 10:47:04 +01:00
4cacc4701d
update plumed support to include version 2.6.0. Fix bug in API check
2020-02-13 16:03:58 +01:00
d024b3d340
Add shared memory optimization
2020-02-12 01:35:44 +03:00
9427fc50a5
Update Colvars library to version 2020-01-27
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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
43a9936241
Fix tagint usage
2020-01-20 03:38:58 +03:00
f69a17dd3a
Reduce unnecessary data exchanges
2020-01-19 02:05:16 +03:00
514271c984
recover compilation with -DLAMMPS_BIGBIG and fix whitespace and formatting issues
2020-01-08 17:57:54 -05:00
18a0cd3ead
Merge pull request #1817 from akohlmey/collected-small-fixes
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Collected small bugfixes and updates
2020-01-08 17:16:34 -05:00
d3eed9dba4
Merge pull request #1752 from ndtrung81/gpu-mem-leak-init
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Fixed bugs with kernel (re)compiling when the global device got clear and reinitialized
2020-01-08 16:17:13 -05:00
6e2c3b7ce9
Merge branch 'master' into collected-small-fixes
2020-01-08 16:14:19 -05:00
481c647889
Merge pull request #1776 from Vsevak/tip4p_gpu
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GPU support for lj/cut/tip4p/long pair style
2020-01-08 15:35:39 -05:00
00dce6b198
Merge branch 'master' into gpu-mem-leak-init
2020-01-08 14:26:03 -05:00
e8a941a0b9
Remove unnecessary data transfer from tip4p/gpu pairstyle init
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Such data transfer is performed at each timestep, so it does not belong to the initialization
2020-01-08 01:48:47 +03:00
66a473455e
silence warnings from generic OpenCL header files (as seen on Fedora 31)
2020-01-06 17:34:26 -05:00
337b0fd649
Fix 'sametag' transfer
2019-12-22 20:20:12 +03:00
4c3ec145f3
Corrected the wrong use of the stubs path in -rpath
2019-12-17 14:05:39 -06:00
7e8a04d985
More minor update to README
2019-12-12 09:57:49 -06:00
99ba15bf6a
Updated README and added -L$(CUDA_HOME)/lib64/stubs to the Makefile's
2019-12-11 16:29:42 -06:00
a3fca53e97
Separate the computation of newsite into another kernel
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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
4a51e1660f
Add thread fence in kernel to fix Volta indeterminacy
2019-12-07 01:16:39 +03:00
a2f9fa8e78
Separate the computation of hneigh into another kernel
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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
66a076b819
Delete "float.h" from TIP4P GPU kernel for better OpenCL compatibility
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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
4febc7f794
Add copyright and fix style
2019-11-18 02:01:32 +03:00
ca8d1ac2ff
Simplify tip4p GPU memory resize using 'resize_ib'
2019-11-18 02:01:32 +03:00
f803ba5655
Add shfl_xor sum to kernel for ARCH>=300
2019-11-12 21:35:36 +03:00
64bdc59623
Implement GPU pair style lj/cut/tip4p/long/gpu
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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
e119bffcca
Fixed bugs with kernel (re)compiling when the global device got cleared and then reinitialized
2019-10-31 01:15:53 -05:00
a0d74ca2ae
Bug fix for gay-berne potential when mu != 1.0.
2019-10-27 22:31:00 -07:00
b631362137
Merge pull request #1735 from ndtrung81/gpu-mem-leak-init
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Gpu mem leak with init invoked multiple times
2019-10-25 17:08:21 -04:00
e7cb2f4cac
put back overly eager deleted code that is used without -DNDEBUG
2019-10-21 03:25:21 -04:00
08b55c4ca5
silence compiler warning
2019-10-20 19:00:54 -04:00
c144b1af71
fix typos
2019-10-20 18:42:22 -04:00
6767fa5604
update supported plumed library to version 2.5.3
2019-10-20 16:27:32 -04:00
67512f8afc
remove bogus POEMS header files from AtC lib folder
2019-10-20 16:13:03 -04:00
b705525734
resolve unused parameter warnings in USER-ATC package
2019-10-20 13:36:06 -04:00
86f644979c
Updated pppm
2019-10-20 00:18:28 -05:00
