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937 Commits

Author SHA1 Message Date
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
Steve Plimpton 5e48565761
Merge pull request #961 from cnegre/newsystem 
Added newsystem flag to be passed to latte
 2018-06-25 17:20:57 -06:00
Axel Kohlmeyer af91f7fa5d LAMMPS does not build on windows without this one 2018-06-25 18:13:41 -04:00
Christian F. A. Negre 0cd86bab22 Added new checksum value 2018-06-25 14:58:49 -06:00
Christian F. A. Negre 2165a2aa9b Changed version on cmakelist and install.py 2018-06-22 10:04:20 -06:00
Steve Plimpton f5f73b0172
Merge pull request #958 from ndtrung81/gpu-updates 
Bug fixes and updates to the GPU package
 2018-06-22 08:52:20 -06:00
Trung Nguyen 28504e91c0 Added missing source files for born/coul/wolf/cs in the gpu library 2018-06-20 15:08:24 -05:00
Trung Nguyen a9b794b2ab Updates to the core-shell gpu pair styles 2018-06-20 10:43:13 -05:00
Trung Nguyen 3ae8fdccd8 Updated the kernels for born/coul/long/cs and coul/long/cs gpu styles 2018-06-19 16:22:00 -05:00
Trung Nguyen 70a7b37614 Updated pair coul/long/cs and born/coul/long/cs; updated gpu neighbor builds to support core-shell styles where r2 can be tiny. 2018-06-19 15:50:02 -05:00
Steve Plimpton fe14bfd1d2
Merge pull request #951 from martok/meam-diaref-fix 
Apply modifications to MEAM & MEAM/C as found by Kyung-Han Kang
 2018-06-18 10:29:57 -06:00
Steve Plimpton 16cc613993
Merge pull request #920 from junghans/mscg 
cmake: add DOWNLOAD_MSCG option
 2018-06-18 10:06:16 -06:00
Trung Nguyen 6842a527e0 Fixed bugs and added born/coul/long/cs/gpu and coul/long/cs/gpu, need tests 2018-06-18 00:15:28 -05:00
Trung Nguyen 265b6c261e Fixed bugs with lj/expand/coul/long and its gpu version 2018-06-15 23:38:37 -05:00
Axel Kohlmeyer fe483a769f update makefiles in lib/linalg to support .F files in addition to .f files 2018-06-15 15:35:34 -04:00
Axel Kohlmeyer f312fbfe32 update Install.py to use a specific numbered release version instead of master 2018-06-15 15:16:10 -04:00
Sebastian Hütter f68c6dddb8 Apply modifications to MEAM & MEAM/C as found by Kyung-Han Kang 2018-06-15 12:33:38 +02:00
Steve Plimpton 661848139c
Merge pull request #926 from ndtrung81/gpu-updates 
some updates to the GPU package
 2018-06-13 12:57:01 -06:00
Christoph Junghans 37268e435b Merge remote-tracking branch 'origin/master' into mscg 2018-06-08 18:06:06 -06:00
ndtrung a4a3133b76 Switched to standard C++ header files for consistency with other source files 2018-06-01 23:13:49 -05:00
Stan Moore c27e617fd8 Add logic to Makefile.kokkos 2018-05-29 11:33:18 -06:00
Stan Moore 1422b0413b Update Kokkos library to v2.7.00 2018-05-25 15:00:53 -06:00
Trung Nguyen 341fa160fe Updated UCL_Device built with OpenCL to use platforms that support accelerators by default 2018-05-23 16:11:55 -05:00
Trung Nguyen 2f9e6d4566 Fixed bugs in lal_device.cpp with node_names dynamically allocated and dipole/long/gpu 2018-05-21 23:32:25 -05:00
Axel Kohlmeyer 4ec31564fe fix preprocessor directive bug in lib/atc 2018-05-21 16:50:16 -04:00
Trung Nguyen 838a1938bb Added pair styles lj/expand/coul/long to USER-MISC and its gpu version to GPU package, added lj/cut/dipole/long/gpu; and added an example Makfile to build GPU package for multi-arch 2018-05-20 17:03:12 -05:00
Christoph Junghans 2e7b919774 linalg: update to netlib lapack-3.7.1 2018-05-18 15:20:47 -06:00
Christoph Junghans 858c211fdc linalg: add functions needed for MSCG 2018-05-18 15:08:08 -06:00
Stan Moore 5a4a7cebc1 Fix performance regression in KOKKOS package 2018-05-16 16:12:05 -06:00
Steve Plimpton bebf25dcb3
Merge pull request #912 from ellio167/kim-update 
Update to kim-api-v1.9.5
 2018-05-14 16:16:18 -06:00
Ryan S. Elliott 09046ad3f7 Update to kim-api-v1.9.5 
Fixes the 'everything' option
 2018-05-12 10:08:09 -05:00
Axel Kohlmeyer 233f03ea8e windows portability bugfix 2018-05-11 18:03:49 -04:00
Axel Kohlmeyer 724ade0af3 silence compiler warnings about bool vs int in AtC lib 2018-05-10 18:48:47 -04:00
Axel Kohlmeyer 40a8b1af79 fix stupid bug in AtC when using alloca() instead of VLAs 2018-05-10 17:42:10 -04:00
Axel Kohlmeyer 79d1d3458e revive lib/atc/Makefile.mpic++ 2018-05-10 15:44:36 -04:00
Axel Kohlmeyer fccc16f42c tune OpenCL for generic architecture by default 2018-05-08 00:50:23 -04:00
Axel Kohlmeyer e7e1827e57 remove variable length arrays in gpu lib 2018-05-08 00:48:53 -04:00
Axel Kohlmeyer 318dfd0613 correct indentation 2018-05-08 00:32:49 -04:00
Axel Kohlmeyer f4d14c96e8 convert poems lib to use c++-style header includes 2018-05-08 00:29:56 -04:00
Axel Kohlmeyer 3394d18a2a convert gpu lib to use c++-style include files 2018-05-08 00:25:10 -04:00
Axel Kohlmeyer ff6507e7b7 convert colvars lib to use c++ style header files 2018-05-08 00:17:57 -04:00
Axel Kohlmeyer fff962646f convert awpmd header include to c++ style 2018-05-08 00:10:20 -04:00
Axel Kohlmeyer f39a8d46d1 convert atc library header files to C++ style 2018-05-08 00:05:18 -04:00
Axel Kohlmeyer 1888b616c4 remove some extra semicolons 2018-05-07 18:04:25 -04:00
Axel Kohlmeyer 104dde27ed eliminate variable length arrays from AtC lib for C++ standard compliance 2018-05-07 17:36:34 -04:00
Axel Kohlmeyer 551ea9694d add VTK config for recent fedora versions 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer f4fbdea0b3 update .gitignore for lib/latte 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 88dca11b3c update colvars dependencies 2018-05-05 02:36:02 -04:00
Axel Kohlmeyer 460e8bd298 add return value to non-void function 2018-05-05 02:35:42 -04:00
Giacomo Fiorin 0c005f5cb0 Small fixes to Colvars library 
Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
 2018-05-02 15:03:56 -04:00
Steve Plimpton 430027465f
Merge pull request #868 from junghans/latte 
cmake: update latte to v1.1.1
 2018-04-13 08:44:59 -06:00
Axel Kohlmeyer 8f1487fbc6 update lib/latte/Install.py to be consistent with CMake config 2018-04-11 11:20:39 -04:00
Axel Kohlmeyer bc49ce611a restore python3 compatibility 2018-04-09 23:08:49 -04:00
Ryan S. Elliott af8e258ebb Revert to previous code without plug-in interface 2018-04-03 17:17:23 -05:00
Ryan S. Elliott 3f3bab4e71 Create KIM_LAMMPS_PlugIn.h & related changes 2018-04-02 11:45:35 -05:00
Ryan S. Elliott f089d8d247 use correct installed kim lib when adding new models 2018-04-02 09:39:44 -05:00
Ryan S. Elliott 25d2f4b1f6 Update pair_kim for v1.9.4 and versatile linking 
Use dlopen instead of directly linking to kim-api
library.  This will allow for easier distribution
of LAMMPS with support for KIM Models.
 2018-04-02 09:39:44 -05:00
Stan Moore 39786b1740 Update Kokkos library to r2.6.00 2018-03-08 10:57:08 -07:00
Axel Kohlmeyer 812572ea97 update dependencies for colvars library 2018-03-07 10:57:56 -05:00
Axel Kohlmeyer 47e2ca6eb2 apply bugfix to reaxff taper function as described in issue #828 2018-03-07 09:52:14 -05:00
Axel Kohlmeyer a1bdea1dd8 avoid division by zero for pair styles meam and meam/c 2018-03-05 14:03:10 -05:00
Giacomo Fiorin f3cf407a21 Collected fixes and updates to Colvars library 
This commit includes several fixes to moving restraints; also added is support
for runtime integration of 2D and 3D PMFs from ABF.

Mostly changes to existing member functions, with few additions in classes not
directly accessible by LAMMPS.  Also removed are calls to std::pow(), replaced
by a copy of MathSpecial::powint().

Relevant commits in Colvars repository:

7307b5c 2017-12-14 Doc improvements [Giacomo Fiorin]
7f86f37 2017-12-14 Allow K-changing restraints computing accumulated work; fix staged-k TI estimator [Giacomo Fiorin]
7c1c175 2017-12-14 Fix 1D ABF trying to do pABF [Jérôme Hénin]
b94aa7e 2017-11-16 Unify PMF output for 1D, 2D and 3D in ABF [Jérôme Hénin]
771a88f 2017-11-15 Poisson integration for all BC in 2d and 3d [Jérôme Hénin]
6af4d60 2017-12-01 Print message when issuing cv delete in VMD [Giacomo Fiorin]
4413972 2017-11-30 Check for homogeneous colvar to set it periodic [Jérôme Hénin]
95fe4b2 2017-11-06 Allow abf_integrate to start in bin with 1 sample [Jérôme Hénin]
06eea27 2017-10-23 Shorten a few constructs by using the power function [Giacomo Fiorin]
3165dfb 2017-10-20 Move includes of colvarproxy.h from headers to files [Giacomo Fiorin]
32a867b 2017-10-20 Add optimized powint function from LAMMPS headers [Giacomo Fiorin]
3ad070a 2017-10-20 Remove some unused includes, isolate calls to std::pow() [Giacomo Fiorin]
0aaf540 2017-10-20 Replace all calls to std::pow() where the exponent is not an integer [Giacomo Fiorin]
 2018-02-23 08:34:53 -05:00
Axel Kohlmeyer 776f588746 add support for UFM pair style support to OpenCL compilation makefile 2018-02-12 18:43:30 +01:00
Steve Plimpton 4af14becb5
Merge pull request #710 from rpleite/add-pair-ufm 
Add the UFM pair potential - (GPU/OPT/OMP)
 2018-02-02 14:38:28 -07:00
Steve Plimpton 1bd9e175e9
Merge pull request #749 from akohlmey/collected-bugfixes-and-updates 
Collected bugfixes and updates for the next patch release
 2018-01-08 09:20:18 -07:00
Axel Kohlmeyer 75f1a4f3f0 use filelink.o consistently, since filelink does not work with some compilers, e.g. nvcc 2018-01-04 20:43:53 -05:00
Stan Moore a2756db66b Update to Kokkos library v2.5.00 2017-12-15 16:42:06 -07:00
Stan Moore da83feb8ca Merge branch 'master' into kk_update 2017-12-15 16:36:21 -07:00
Axel Kohlmeyer 319508bd29 fix scoping ambiguity issue that confuses nvcc 2017-11-30 10:56:58 -05:00
Stan Moore 7d07f062b6 Remove const from variable 2017-11-20 10:21:19 -07:00
Stan Moore f3ed148828 Fix for big endian machines 2017-11-20 10:18:53 -07:00
Steve Plimpton c4c59b909e
Merge pull request #716 from akohlmey/collected-small-changes 
Collected small changes and bugfixes for next patch
 2017-11-13 09:00:26 -07:00
Stan Moore 88474fc5c2 Remove Kokkos tpls directory 2017-11-06 13:48:26 -07:00
Stan Moore 16b5315845 Update Kokkos to v2.04.11 2017-11-06 13:47:33 -07:00
Axel Kohlmeyer b34000a5e1 make *_gpu_reinit() functions consistent in returning void. correct prototypes in src/GPU, too. 
this supersedes and closes #719
 2017-11-04 02:49:22 -04:00
Axel Kohlmeyer 2dbb44f2c6 provide Makefile.lammps template for use with bundled linalg lib 2017-10-24 13:38:04 -04:00
Axel Kohlmeyer d1630bbe34 add missing BLAS/LAPACK functions used by LATTE to linalg lib 2017-10-24 13:22:20 -04:00
Rodolfo Leite 941ee565a1 Added lal_ufm_ext.cpp in lib/gpu 2017-10-24 11:12:51 -02:00
Rodolfo Leite b63acf6843 Added the UFM files (doc/src - lib/gpu - src) 2017-10-24 11:11:10 -02:00
Giacomo Fiorin f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
Giacomo Fiorin 6e7504f153 Import segfault fix in Colvars module 2017-10-19 08:09:44 -04:00
Giacomo Fiorin 3e89b270fd Update Colvars to version 2017-10-11 
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
 2017-10-13 13:45:10 -04:00
Steve Plimpton 18ca2292c2 Merge pull request #686 from giacomofiorin/lepton-library 
Add Lepton library within lib/colvars
 2017-10-13 09:48:42 -06:00
Giacomo Fiorin d90aad887e Add Lepton library within lib/colvars 2017-10-09 15:25:43 -04:00
Ryan S. Elliott 775a15b9da Update lib/kim for kim-api-v1.9.2 2017-10-09 14:06:30 -05:00
Steve Plimpton 439c2fd980 Merge pull request #677 from stanmoore1/kk_update 
Update to Kokkos r2.04.04 and add workaround for performance regression
 2017-10-05 17:10:00 -06:00
Stan Moore a55adf4a68 Update to Kokkos r2.04.04 and add workaround for performance regression 2017-10-03 11:30:00 -06:00
Axel Kohlmeyer e6969002ce having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc 2017-09-25 19:37:37 -04:00
Steve Plimpton ee487ef4aa Merge pull request #652 from junghans/latte 
Add LATTE fix
 2017-09-22 10:32:19 -06:00
Steve Plimpton a8ae886667 update fix latte examples and virial 2017-09-21 10:40:54 -06:00
Steve Plimpton dd49d54889 new SNAP potentials and examples 2017-09-20 08:54:30 -06:00
Axel Kohlmeyer 59d2e13d48 add .gitignore and add Makefile.lammps.* symlinks to stay consistent with other libraries 2017-09-19 19:06:02 -04:00
Steve Plimpton ac897ea645 LATTE package doc update and some small code changes 2017-09-19 16:27:25 -06:00
Axel Kohlmeyer be96486d66 compile all objects in the GPU library with -fPIC for building shared object 2017-09-19 11:24:48 -04:00
Axel Kohlmeyer 48dd824b26 ignore generated header files with OpenCL kernels 2017-09-19 11:24:38 -04:00
Christoph Junghans 02665e45a4 fix doc in lib/latte/Makefile.lammps.* 2017-09-15 17:52:14 -06:00
Christoph Junghans 17aeccf19f Merge remote-tracking branch 'origin/master' into latte 2017-09-15 16:18:13 -06:00
Giacomo Fiorin f1fce64ff9 Fix small typo to calculation of accumulated work in Colvars 2017-09-14 12:58:00 -04:00
Steve Plimpton f971cd6e45 Merge pull request #647 from rbberger/gpu_opencl_2 
Use OpenCL 2.x API in GPU package when supported
 2017-09-12 10:56:13 -06:00
Steve Plimpton e927794696 Merge pull request #643 from andeplane/gpu_opencl_compile_fix 
Fixed OpenCL compilation issues with __global keywords
 2017-09-12 10:31:22 -06:00
Richard Berger 84b84c10db Use OpenCL 2.x API in GPU package when supported 2017-09-09 19:53:56 -04:00
Christoph Junghans 2f6be88c4a Merge remote-tracking branch 'origin/master' into exaalt 2017-09-08 07:04:12 -06:00
Richard Zamora 7b1542a0ba merging stable and exaalt branches into exaaltstable 2017-09-07 16:31:50 -06:00
Anders Hafreager dbc60d949f Fixed OpenCL compilation issues with __global keywords 2017-09-06 15:08:02 +02:00
Stan Moore cbf3646806 Merge branch 'master' into USER-DPD_kokkos 2017-08-23 15:20:56 -06:00
Steve Plimpton b6c93f96cf Merge pull request #629 from stanmoore1/kokkos_update 
Update Kokkos library to v2.04.00
 2017-08-23 14:39:42 -06:00
Axel Kohlmeyer e88ff8d6f9 correct embedded help for GPU lib Install.py 2017-08-23 15:20:30 -04:00
Stan Moore 5c985946d5 Merge branch 'master' into USER-DPD_kokkos 2017-08-22 13:50:19 -06:00
Stan Moore 090c792d90 Update Kokkos library to v2.04.00 2017-08-22 13:42:02 -06:00
Steve Plimpton c46d5ff422 Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10 
Minor fixes to Colvars module
 2017-08-17 11:32:38 -06:00
Steve Plimpton dd67989c76 Merge pull request #601 from stanmoore1/kokkos_update 
Update Kokkos library to v2.03.13
 2017-08-17 11:32:18 -06:00
Steve Plimpton 00aafef1a8 Merge pull request #597 from ndtrung81/three-body-short-nlist 
Implementing short neighbor lists for three-body gpu styles
 2017-08-17 11:31:59 -06:00
Tim Mattox 4041db8d1a Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17 2017-08-11 13:25:28 -04:00
Axel Kohlmeyer c6d923b6c8 make download function more resilient by also catching failed execution 2017-08-10 21:15:35 -04:00
Axel Kohlmeyer 6d24be8bb7 whitespace cleanup 2017-08-10 21:14:40 -04:00
Giacomo Fiorin da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
Axel Kohlmeyer 146aa4cdbd fall back to wget when curl is not available 2017-08-10 09:05:23 -04:00
Axel Kohlmeyer 2f3747eb6e we need to override compiler flags in lib/voronoi/Install.py 
The default compiler flags in voro++'s config.mk file do not include
-fPIC, which makes it incompatible with building the shared object for
the python wrapper.
 2017-08-10 08:34:46 -04:00
Axel Kohlmeyer 2bc6ad80d4 avoid writable string and deprecated implicit conversion warning 2017-08-10 07:45:21 -04:00
Axel Kohlmeyer 6780c73907 restore mpic++ makefile to resolve regression test failure 2017-08-09 07:10:08 -04:00
Axel Kohlmeyer b7b1257b01 remove attempts to use urllib and use curl for all downloading. restore printing help with no flags. 2017-08-08 17:00:09 -04:00
Axel Kohlmeyer 30431d4edb rework Install.py for gpu library. make it consistent with other lib folders and support python3 2017-08-08 16:57:27 -04:00
Stan Moore 8a7a831bd6 Remove redundant check in Makefile.kokkos 2017-08-08 12:57:22 -06:00
Axel Kohlmeyer c53a84a967 update README file for lib/mscg 2017-08-08 13:55:12 -04:00
Axel Kohlmeyer d2b0c287d2 add local makefile overrides to be compatible with standard suffixes 2017-08-08 13:19:44 -04:00
Axel Kohlmeyer b3244f9c98 more lib compilation updates 2017-08-08 07:20:33 -04:00
Axel Kohlmeyer 8bba29d91e more lib installation cleanup 2017-08-07 17:21:45 -04:00
Axel Kohlmeyer 135b1650f1 revamp of library builds 
- remove cross compiler stuff
- make use of Install.py consistent
- provide options for Makefile.serial and Makefile.mpi that match those in src
 2017-08-07 17:13:01 -04:00
Axel Kohlmeyer 163ed27618 update .gitignore 2017-08-04 16:10:59 -04:00
Axel Kohlmeyer 23ca0099f7 more updates to kim/Install.py to restore missing functionality and align with other scripts 
- build into local directory to replace existing installation is now default
- add wrapper function that calls curl in case python package has not ssl support
- have to specify -n flag to avoid wiping out the existing installation
- can specify -p to point to an existing kim-api installation (implies -n)
 2017-08-04 14:47:32 -04:00
Stan Moore 8431ca5fec Remove tpls directory 2017-07-31 10:54:07 -06:00
Stan Moore 13f2d39f55 Update Kokkos library to v2.03.13 2017-07-31 10:34:21 -06:00
Axel Kohlmeyer 9bfd9267fa update and automate the QUIP configuration so that no environment variables are needed 2017-07-28 16:11:13 -04:00
Axel Kohlmeyer 3ebf561e0d remove tarball after unpacking 2017-07-28 14:25:47 -04:00
Axel Kohlmeyer ffb778cf9b make Install.py for lib/smd and lib/voronoi consistent 2017-07-28 14:03:29 -04:00
Axel Kohlmeyer f3850da9fe clean up makefiles provide "serial" and "mpi" targets for atc and awpmd 2017-07-28 13:36:06 -04:00
Axel Kohlmeyer e7d9aabca6 Merge branch 'kim-install' into install-and-docs-reviewed 2017-07-28 11:25:08 -04:00
Stan Moore 9695aa6092 Merge branch 'master' into USER-DPD_kokkos_testing 2017-07-27 15:51:56 -06:00
Axel Kohlmeyer c494ec35e2 correct symbolic links to shared Install.py file 2017-07-27 12:48:32 -04:00
Axel Kohlmeyer acf6d54ec1 python3 port, yet untested 2017-07-27 09:25:39 -04:00
Axel Kohlmeyer 0427f6205e fix typo 2017-07-27 09:25:02 -04:00
Axel Kohlmeyer da7a5f55d3 Merge branch 'kim-install' into install-and-docs-reviewed 2017-07-26 19:32:55 -04:00
Axel Kohlmeyer 715c797df0 simplify Install.py for voronoi 2017-07-26 15:14:12 -04:00
Axel Kohlmeyer fd6e11f821 convert copies of Install.py files to symlinks 2017-07-26 14:29:52 -04:00
Axel Kohlmeyer f7a243a4d9 convert explicit copies back into symbolic links 2017-07-26 14:20:03 -04:00
Axel Kohlmeyer f0d286358e must not include system headers within 'extern "C"' blocks. breaks with MPICH 2017-07-26 14:02:02 -04:00
Stan Moore bc446bb8b0 Merge branch 'master' into USER-DPD_kokkos_testing 2017-07-25 12:12:30 -06:00
Trung Nguyen aa60ef6ed8 Cleaned up 3-body kernels, reverted some mistaken changes to vashishta 2017-07-23 00:08:55 -05:00
Trung Nguyen a71f5a0c20 Enabled again neigh no with tpa > 1 for 3-body gpu styles for backward compatibility, could be slower than neigh no tpa 1 in many cases 2017-07-22 22:57:37 -05:00
Trung Nguyen 3d1d0c58c7 Cleaned up 3-body gpu styles, and fixed a bug for tersoff/zbl/gpu. 
There is a unresolved bug for neigh no with tpa > 1 with BaseThree, enforce tpa = 1 for neigh no in BaseThree for now.
 2017-07-21 12:08:04 -05:00
Axel Kohlmeyer 1b704bab18 Merge branch 'colvars-safer-makefiles' of https://github.com/giacomofiorin/lammps into colvars-quickfix 2017-07-20 15:59:23 -04:00
Giacomo Fiorin c98f6140e7 Change order of targets in Makefiles for Colvars 2017-07-20 15:49:31 -04:00
Giacomo Fiorin 5031f5b807 Comment out use by Colvars of Makefile.lammps from other packages 2017-07-20 15:48:10 -04:00
Axel Kohlmeyer 9d0d90c038 README clarification from giacomo 2017-07-20 15:25:27 -04:00
Axel Kohlmeyer 66154e8a8b avoid makefile failure, if LAMMPS has not been configured yet 2017-07-20 15:05:58 -04:00
Ryan S. Elliott 84065dde21 Refactor lib/kim/Install.py; works with phtyon 3 2.7 2017-07-20 12:02:50 -05:00
Giacomo Fiorin ef9fb944c7 Detect number of processors for make 2017-07-20 10:53:08 -04:00
Giacomo Fiorin 187a80be77 Add forgotten decode() in Install.py 2017-07-19 22:21:49 -04:00
Axel Kohlmeyer 355aad9691 restore python3 support. this now can run with python 2.7.13 and 3.5.3. 2017-07-19 17:19:44 -04:00
Giacomo Fiorin ee6cac826e Update Colvars to version 2017-07-15 and support automated builds for it 2017-07-19 14:24:07 -04:00
Ryan S. Elliott f181a0bfab Update lib/kim/Install.py for phthon 2.7 conversion 2017-07-19 12:54:33 -05:00
Axel Kohlmeyer 81f342aafa fix variable name bug and synchronize with other ported Install.py files 2017-07-18 18:06:18 -04:00
Axel Kohlmeyer 7ccb0d37cd port USER-SMD folder. make voronoi consistent with it 2017-07-18 17:37:48 -04:00
Axel Kohlmeyer 03cd4c5255 ported lib/voronoi/Install.py to python 3.x and tested with 2.7 2017-07-18 17:16:10 -04:00
Richard Berger d7355801df Make KIM Install.py Python 3 compatible 2017-07-15 12:03:04 -05:00
Steve Plimpton 296e572e69 better Install.py script for KIM from Ryan Elliott 2017-07-14 16:25:16 -06:00
Trung Nguyen cdac5f496c Built 3-body short neighbor list for the 3-body kernels using per-pair cutoffs for vashishta gpu style 2017-07-11 00:13:56 -05:00
Trung Nguyen 8c9db3ea00 Built 2-body short neighbor list and used for 2-body kernels in tersoff gpu styles 2017-07-10 23:50:21 -05:00
Ryan S. Elliott e30c5fc956 Fixed shebang and renamed to lib/kim/Install.py 2017-07-10 21:05:29 -05:00
Ryan S. Elliott c29e8fba9b Updated lib/kim/README file to go along with new install.py 2017-07-10 17:00:30 -05:00
Ryan S. Elliott 8d592f4b9e Finalized code for lib/kim/install.py 2017-07-10 16:43:23 -05:00
Trung Nguyen ea2b01e83b Refactored 3-body gpu styles to remove code duplication 2017-07-08 20:17:31 -05:00
Trung Nguyen 34fe2273f6 Added short neighbor list implementation for tersoff/zbl/gpu and tersoff/mod/gpu 2017-07-08 14:59:48 -05:00
Trung Nguyen 77c60189b8 Minor cleanups for tersoff/gpu 2017-07-08 14:43:53 -05:00
Trung Nguyen 1c6533e53d Working on short neighbor list for tersoff/gpu 2017-07-08 14:15:26 -05:00
Trung Nguyen 68206079da Supported short neighbor lists for 3-body kernels in sw/gpu and vashishta/gpu 2017-07-07 16:47:24 -05:00
Ryan S. Elliott b0be8b24ea Further work on lib/kim/install.py 2017-07-06 15:50:03 -05:00
Ryan S. Elliott 16fc2d6fe1 Add install.py and update config for kim lib 2017-07-06 15:49:58 -05:00
Stan Moore da0dcbe0bb Updating to master 2017-06-19 10:56:24 -06:00
sjplimp d3c90f3c14 Merge pull request #510 from akohlmey/collected-small-changes 
Collected small changes
 2017-06-15 11:12:14 -06:00
sjplimp 7227bc415d Merge pull request #526 from andeplane/vashishta_gpu 
Implemented pair style vashishta in GPU package
 2017-06-15 08:52:13 -06:00
Anders Hafreager d7646aeeed Fixed opencl error 2017-06-14 12:03:47 +02:00
Anders Hafreager 5f9341813d Removed debug output 2017-06-14 10:57:54 +02:00
Anders Hafreager 8441307185 Removed non-general CUDA-dir in makefile 2017-06-14 10:28:46 +02:00
Anders Hafreager 720af5c360 Added vashishta to OpenCL makefile 2017-06-14 10:27:52 +02:00
Anders Hafreager eeff0b8633 Added vashishta GPU package for NVidia 2017-06-14 10:24:16 +02:00