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822 Commits

Author SHA1 Message Date
Axel Kohlmeyer 4adbacf8e5 Merge branch 'python-script-portability' into collected-post-stable-patches 2018-12-03 19:14:47 -05:00
Giacomo Fiorin d603d084c4 Fix typo, whitespace cleanup 2018-12-03 18:12:10 -05:00
Giacomo Fiorin 46c0be57de Restore deleted deps file (if deletion is intentional, please delete again) 2018-12-03 18:08:27 -05:00
Axel Kohlmeyer db2c8887cf Merge branch 'python-script-portability' into collected-post-stable-patches 2018-12-03 17:50:47 -05:00
Axel Kohlmeyer e5c555fa7d consolidate shared code from various Install.py files into install_helpers.py 2018-12-03 17:50:20 -05:00
Axel Kohlmeyer 98728cddbe Merge remote-tracking branch 'devel/python-script-portability' into collected-post-stable-patches 2018-12-03 15:18:03 -05:00
Axel Kohlmeyer e4ca5b1889
Merge pull request #1232 from akohlmey/collected-small-fixes 
First chunk of collected small fixes for the stable release
 2018-11-29 18:19:12 -05:00
Axel Kohlmeyer cda3227b05 plug memory leak in poems library 2018-11-29 16:41:11 -05:00
Axel Kohlmeyer 6705777f7b fix memory issue in POEMS library, where auxiliary data was cast to a data structure of different (smaller) size when deleting. 
this commit adds support to a callback function that allows to delete aux data in the Tree with its native size.
 2018-11-29 16:34:41 -05:00
Axel Kohlmeyer eda79bd1c2 use shutil.rmtree() instead of calling 'rm -rf' for increased portability 2018-11-28 20:46:50 -05:00
PabloPiaggi 22e774adef Revert "Add --noinstall flag to use the plumed source code directly without issuing make install" 
This reverts commit a4684e2629.

Revert --noinstall flag commit
 2018-11-28 17:37:24 +01:00
Michele Invernizzi 8213287966 detect the number of available CPU for plumed make, as suggested by @akohlmey 2018-11-28 16:09:05 +01:00
PabloPiaggi a4684e2629 Add --noinstall flag to use the plumed source code directly without issuing make install 2018-11-28 15:43:35 +01:00
Michele Invernizzi 3d5423f5da revert back to correct path to Plumed.inc.*. (my fault, I was not doing the 'make install') 2018-11-28 09:18:38 +01:00
Michele Invernizzi 32abe35201 added -j8 option for faster plumed make 2018-11-28 00:08:55 +01:00
Michele Invernizzi c87bdda9a8 fixed wrong path to Plumed.inc.* 2018-11-28 00:08:01 +01:00
Michele Invernizzi 1b50ad02fb fixed uninitialized var homedir 2018-11-28 00:06:50 +01:00
Axel Kohlmeyer f254b8e3a3
Merge pull request #1226 from akohlmey/cmake-gpu-enhancements 
Enhancements for using CMake with the GPU package, improved compatibility with cmake 3.x versions, improved handling of shared library building.
 2018-11-27 16:05:47 -05:00
Axel Kohlmeyer 05fb2d7587 more generated files/symlinks to ignore 2018-11-26 18:23:06 -05:00
Axel Kohlmeyer 5df2f92651 minor cleanup in lib/gpu 2018-11-26 18:22:33 -05:00
Axel Kohlmeyer e0ff230268 remove comment-in-comment 2018-11-26 17:03:48 -05:00
Axel Kohlmeyer a91d89b516 avoid array overflows and silence compiler warnings from unused parameters 2018-11-21 09:24:10 -05:00
Axel Kohlmeyer 421f97e444
Merge pull request #1214 from akohlmey/collected-small-changes 
Collected small changes and many spelling fixes for next release candidate
 2018-11-20 10:34:58 -05:00
Axel Kohlmeyer a7bfb30043 update atc/cauchy_born examples with missing files 2018-11-16 23:03:47 -05:00
Giacomo Fiorin 11de8dafe3 Update Colvars library to version 2018-11-16 
Fixes several issues with running averages and time correlation function
computations.  Details are in:

https://github.com/Colvars/colvars/issues/143
https://github.com/Colvars/colvars/issues/193
https://github.com/Colvars/colvars/pull/194
 2018-11-16 09:57:07 -05:00
Axel Kohlmeyer 090778c42b
Merge pull request #1204 from lammps/doc-plumed 
Linkage mode improvements and documentation updates for USER-PLUMED package
 2018-11-15 13:48:58 -05:00
Axel Kohlmeyer 04520e627d add code and scripts to support all three plumed linkage modes with fix plumed for conventional build 2018-11-14 21:26:36 -05:00
Stan Moore c22c6e4d34 Add LAMMPS changes to Kokkos Makefile 2018-11-12 15:30:14 -07:00
Stan Moore b2d67bcbb5 Remove tpls dir 2018-11-12 15:18:06 -07:00
Stan Moore b3f08b38a2 Update Kokkos library in LAMMPS to v2.7.24 2018-11-12 15:16:26 -07:00
Axel Kohlmeyer a6e9b99295
Merge pull request #1180 from gtribello/master 
Add natively supported PLUMED interface to LAMMPS
 2018-11-08 16:16:50 -05:00
Ryan S. Elliott 9ed6f2fc43 Adjust lib/kim install script and settings 2018-11-04 20:10:04 -06:00
Axel Kohlmeyer badfdd7433 download only the plumed-src package and include further tweaks to be compatible with plumed 2.5b 2018-11-03 00:21:10 -04:00
Axel Kohlmeyer 54c52c3bdf adjust compilation settings to link in plumed library statically and all its dependencies 2018-11-02 22:52:36 -04:00
Giacomo Fiorin 85a5cab663 Update Colvars library to version 2018-10-16 2018-11-02 17:45:20 -04:00
Ryan S. Elliott b0938b70d5 Merge branch 'master' into kim-v2-update 2018-11-01 19:41:13 -05:00
Axel Kohlmeyer 2a5cd1d31e remove debug output 2018-10-31 00:16:44 -04:00
Axel Kohlmeyer 42068944aa Merge branch 'master' of github.com:gtribello/lammps into fix-plumed 2018-10-30 20:43:49 -04:00
Axel Kohlmeyer e3b89b60dc add checksum support for downloaded tar archives. upgrade to v2.4.3 2018-10-30 20:43:20 -04:00
Christoph Junghans 044507640f include Plumed.h with full path 2018-10-29 06:52:19 -06:00
Axel Kohlmeyer 283096d1d5 update .gitignore 2018-10-29 03:50:55 -04:00
Axel Kohlmeyer 360aca581c remove last reference to voro++ 2018-10-28 21:56:49 -04:00
Axel Kohlmeyer bfbf5695fd adjust path for includelink to find the Plumed.h wrapper properly 2018-10-28 21:30:37 -04:00
Axel Kohlmeyer a60b6d1ab8 add feature to python lib install script to support existing installation and use links 2018-10-28 18:12:32 -04:00
Gareth Tribello ff9f836be4 Merge remote-tracking branch 'upstream/master' 2018-10-26 22:01:05 +01:00
Ryan S. Elliott f61f43a56b Merge branch 'master' into kim-v2-update 2018-10-01 21:17:26 -05:00
Ryan S. Elliott 634ed487a5 Use pkg-config to find kim-api-v2 library settings 2018-09-04 22:43:55 -05:00
Richard Berger ff2e13e063 Merge branch 'master' into ScaFaCoS 2018-09-04 21:35:46 -04:00
Ryan S. Elliott 796b6b2d9c Merge branch 'master' into kim-v2-update 2018-08-24 14:28:33 -05:00
Steven J. Plimpton 89a3670fb5 merge master into cslib branch, update docs 2018-08-22 11:19:55 -06:00
Steven J. Plimpton c4b55385e2 doc updates 2018-08-22 10:40:39 -06:00
Steven J. Plimpton 9a15d0bd83 Merge branch 'master' into scafacos 2018-08-22 09:25:29 -06:00
Steven J. Plimpton c719af8bcd remove wrong link optimization flag 2018-08-20 13:42:34 -06:00
Steven J. Plimpton f73ffb829b add a needed ifort flag for LAMMPS/LATTE link 2018-08-20 11:20:23 -06:00
Ryan S. Elliott d0667d21cc Merge branch 'master' into kim-v2-update 2018-08-18 12:23:19 -05:00
Steve Plimpton ccacf0d4bb
Merge pull request #1048 from lammps/doc-reorg-start 
Documentation Refactoring: Section Start
 2018-08-15 15:25:17 -06:00
Steven J. Plimpton 9c3748e07c change Python.txt to Python_head.txt, adapt GPU package syntax 2018-08-15 07:31:31 -06:00
Richard Berger ad9126f30e Kokkos bugfix for building with cmake 2018-08-14 22:19:20 -04:00
Steven J. Plimpton 7ec52784cb more changes to doc pages and CMakeLists.txt 2018-08-14 15:44:25 -06:00
Steven J. Plimpton 781ddc07c7 update to CSlib website link 2018-08-13 15:29:28 -06:00
Richard Berger 65d11171c4 Replace functions which were deprecated since CUDA 5 2018-08-09 03:36:21 -04:00
Richard Berger 6d60075d3b GPU Package: Use __shfl_xor_sync starting with CUDA 9 2018-08-09 02:33:35 -04:00
Rene Halver fc93a79fdd updated to support ScaFaCoS 1.0.1 2018-08-08 14:05:28 -06:00
Rene Halver 76ad2b35a9 Merge remote-tracking branch 'origin/master' into ScaFaCoS 2018-08-08 09:53:32 -06:00
Steve Plimpton 985318203d
Merge pull request #1038 from stanmoore1/issue-1037 
KOKKOS Package bugfix: Workaround for issue #1037
 2018-08-08 08:42:21 -06:00
Richard Berger ac7aeb6862 Add extra check for OpenCL timers 
Fixes issue #1034 by preventing time() to access non-existent OpenCL events
 2018-08-07 21:43:59 -04:00
Rene Halver 953b283773 updated URL for tarball download 2018-08-06 15:59:46 -06:00
Stan Moore 32917f4caa Workaround for issue 1037 2018-08-06 10:50:06 -06:00
Rene Halver e8774dce97 removed thread restriction on make command, should make the building process faster 2018-08-03 11:31:11 -06:00
Christoph Junghans 463e34cef5 Merge remote-tracking branch 'origin/master' into HEAD 2018-08-03 08:13:12 -06:00
Rene Halver efaebe0eb0 READMEs for USER-SCAFACOS completed 2018-08-02 13:44:12 -06:00
Rene Halver a8f0200fe9 Install.py works on dummy tar-ball 2018-07-31 13:33:10 -06:00
Steve Plimpton 8d49d1a8c5
Merge pull request #1010 from lammps/latte-checksum 
new checksum for LATTE download
 2018-07-25 08:42:35 -06:00
Steven J. Plimpton a4dbac63d3 more updates to the new MESSAGE package 2018-07-24 17:22:15 -06:00
Steven J. Plimpton 1aa8307fa1 change CSlib files to BSD license 2018-07-24 12:04:23 -06:00
Steven J. Plimpton 2f55981224 new MESSAGE package for client/server/coupling 2018-07-23 15:58:33 -06:00
Axel Kohlmeyer 923ae041dc (temporary) workaround for memory leaks with OpenCL and MPI for upcoming stable release 2018-07-23 15:52:42 -04:00
Steven J. Plimpton 40dcfa44c9 new checksum for LATTE download 2018-07-23 08:35:40 -06:00
Ryan S. Elliott 6ab93b52bc Merge remote-tracking branch 'lammps/master' into kim-v2-update 2018-07-23 09:30:43 -05:00
Trung Nguyen 644888d03c Fixed bugs with time_q and time_quat not calling start() and stop() when _charge and/or _rot in Atom are true for OpenCL builds 2018-07-22 15:12:45 -05:00
Trung Nguyen b612c7ee75 Fixed a copy-paste bug in lal_neighbor.cpp for neigh no 2018-07-22 13:15:01 -05:00
Trung Nguyen d71e037c23 Renamed dev_acc to dev_ilist for better description and updated the 3-body styles accordingly; also fixed bugs with accessing dev_packed from the three_end kernel of tersoff/mod and tersoff/zbl gpu styles for OpenCL builds 2018-07-22 11:27:14 -05:00
Trung Nguyen 94da4be922 Fixed bugs for tersoff gpu styles for OpenCL builds 2018-07-21 13:50:10 -05:00
Trung Nguyen 01c27194d4 Fixes for lal_neighbor.cpp for get_host() and for time_kernel 2018-07-21 00:18:30 -05:00
Trung Nguyen 223de57401 Added set_platform_accelerator() for nvd_device.h for OpenCL compatibility 2018-07-21 00:14:31 -05:00
Steve Plimpton 884e72a4ba
Merge pull request #1008 from akohlmey/support-platform-select 
OpenCL related fixes and improvements to the GPU package
 2018-07-20 14:32:49 -06:00
Axel Kohlmeyer de8176b4fc various minor OpenCL related fixes and improvements to the GPU package 
- document previously undocumented OpenCL tune settings
- implement OpenCL platform selection through prefixing the device type with the platform id separated by a colon
- allow passing custom tune parameters though postfixing the device type with the 13 tuneable parameters separated by commas
- remove an extra clear() that would delete device properties structs an cause LAMMPS to output garbage strings
 2018-07-20 14:41:54 -04:00
Richard Berger 2eb8d779e8 Fixes a memory leak when using OpenCL 
The GPU package uses OpenCL events for measuring time. These have to be
released to free up memory. I removed the clReleaseEvent() calls in the
clear() method because in some cases they don't exist yet and I couldn't
find a way to check for a valid event (clRetainEvent didn't work). This
at least fixes the massive leak during simulations.

See issue #1006
 2018-07-18 18:54:57 -04:00
Steven J. Plimpton a62b65096b more error checks for Scafacos usage 2018-07-18 15:48:17 -06:00
Steven J. Plimpton b0c9fde1dd more changes from Steve 2018-07-18 15:32:03 -06:00
Steven J. Plimpton e7f4e059cf convert to KSspace style rather than fix 2018-07-13 16:46:06 -06:00
Ryan S. Elliott 67e6afaab2 Update to KIM kim-api-v2.0.0-beta.1 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 5bdc295331 Add skin to pair_kim neigh-list cutoffs & update docs 2018-07-11 15:09:58 -07:00
Ryan S. Elliott 955fe583d8 Updated docs for new pair_kim 2018-07-11 15:09:57 -07:00
Ryan S. Elliott 8bbba22867 First working version of pair_kim with kim-api-v2 2018-07-11 15:09:28 -07:00
Gareth Tribello 4734bc09dc Added descriptions of static linking of PLUMED to README files 2018-07-11 21:56:08 +01:00
Gareth Tribello 492e945b5a Added options to link plumed statically 2018-07-11 16:39:52 +01:00
Axel Kohlmeyer ad4f61a5ce update fatbin makefile for libgpu.a to latest additions 2018-07-10 09:07:54 -04:00
Axel Kohlmeyer 08552fefe9 add md5 checksum support to Install.py for LATTE 2018-06-27 16:52:28 -04:00
Steven J. Plimpton 49a91db0b2 small changes to last LATTE PR, including xControl to upper case 2018-06-25 17:43:31 -06:00