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905 Commits

Author SHA1 Message Date
Axel Kohlmeyer 2d93a713e2
Merge branch 'master' into collected-small-changes 2019-07-30 14:14:11 -04:00
Axel Kohlmeyer 3fdadb5875
add configuration for linking VTK 7.1 on Ubuntu 18.04 2019-07-30 06:02:47 -04:00
Axel Kohlmeyer 7ab7691c51
update PLUMED support to version 2.5.2 2019-07-30 05:57:57 -04:00
Axel Kohlmeyer 6833d6def6
Merge branch 'master' into kim-simulator-models 
# Resolved Conflicts:
#	src/KIM/kim_query.cpp
#	src/KIM/pair_kim.cpp
 2019-07-29 20:43:10 -04:00
Axel Kohlmeyer 0f10c55c1c
avoid recursive header inclusion 2019-07-26 17:26:59 -04:00
Axel Kohlmeyer d59737299c
whitespace cleanup 2019-07-24 16:02:49 -04:00
Ryan S. Elliott be86db9dd9 Update /lib/kim stuff 2019-07-23 21:06:02 -05:00
Axel Kohlmeyer 320be3bcef
undo changes to poems library and package as they fail regression testing 2019-07-22 14:22:36 -04:00
Axel Kohlmeyer 68626f577b
Merge branch 'master' into improve-include-consistency 2019-07-12 19:59:56 -04:00
Axel Kohlmeyer e832b5d50b
make clang++ happy when trying to compile the GPU library 2019-07-12 15:42:16 -04:00
Axel Kohlmeyer 06dcc9e283
Merge branch 'master' into improve-include-consistency 
# Conflicts:
#	src/USER-MESO/atom_vec_tdpd.cpp
 2019-07-09 14:50:00 -04:00
Trung Nguyen 46a9772a6d Minor clean-up 2019-07-05 12:12:29 -05:00
Axel Kohlmeyer d07a49aeea
add missing prototypes 2019-07-05 11:37:21 -04:00
Trung Nguyen 49f27573a7 Fixed a bug in lj96 involving missing the special_lj factor 2019-07-03 23:44:33 -05:00
Axel Kohlmeyer e63fe1fe84
please POEMS library in namespace POEMS and remove "using namespace" from headers 2019-07-04 00:09:01 -04:00
Axel Kohlmeyer 42c31227d9
continuing to clean up include file lists 2019-07-01 15:59:16 -04:00
Axel Kohlmeyer 39f5b8c734
transform POEMS library to conform to IWYU conventions 2019-07-01 04:16:00 -04:00
Stan Moore ea2e73119d Update Kokkos library in LAMMPS to v2.9.00 2019-06-28 11:23:24 -06:00
Christoph Junghans 8c3d18520d add missing include needed on ppc64le 2019-06-26 10:45:31 -06:00
Axel Kohlmeyer 2f29bd29f4
Merge pull request #1430 from ndtrung81/gpu-neigh-hybrid 
Enable neighbor build on the device for pair hybrid substyles
 2019-06-17 14:12:40 -04:00
Axel Kohlmeyer b3f4e2055e
Merge pull request #1438 from giacomofiorin/colvars-update 
Update Colvars library to version 2019-04-26
 2019-05-06 12:08:50 -04:00
Giacomo Fiorin 7e00acce53 Update Colvars library to version 2019-04-26 
The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
 2019-04-30 13:46:37 -04:00
Richard Berger 8145c5028d Fix OpenCL compilation errors due to bad comments in macros 2019-04-30 00:44:12 -04:00
Trung Nguyen 4a4297591e Did some more cleanups 2019-04-17 12:04:31 -05:00
Trung Nguyen 1f43efc111 Cleaned up the changes in Device and the base class of the pair styles 2019-04-17 00:09:49 -05:00
Trung Nguyen c55009a0ac Enabled neighbor list build on the device with pair_style hybrid and hybrid/overlay 2019-04-16 23:30:25 -05:00
Axel Kohlmeyer c52a330a79
update USER-PLUMED support for version 2.5.1 and fix bug in Install.py script 2019-04-04 14:19:53 -04:00
Axel Kohlmeyer 265ad4512d
add sanity check on plumed pre-installed path location 2019-04-04 13:18:27 -04:00
Axel Kohlmeyer 1696432e82
resolve conflict between src/STUBS/mpi.h and lib/message/cslib/src/STUBS_MPI/mpi.h 2019-04-03 01:00:53 -04:00
Ryan S. Elliott 9d0e518cc5 Updates for kim-api-2.0.2 release 2019-03-28 15:35:22 -05:00
Axel Kohlmeyer 2f20581b29
Merge pull request #1374 from akohlmey/collected-small-fixes 
Collected small changes for the next patch release
 2019-03-25 13:15:45 -04:00
Axel Kohlmeyer cd6b23d104
explicitly request OpenCL version 1.2 compatibility when compiling GPU package kernels for OpenCL 2019-03-22 09:50:31 -04:00
Axel Kohlmeyer 741a7fe630
final touches to support compiling with libcurl transparently 2019-03-19 15:40:49 -04:00
Ryan S. Elliott b628e3b1b6 Update openkim.org urls in various places 2019-03-06 10:26:03 -06:00
Ryan S. Elliott 54e5c76333 Bump KIM API version to 2.0.1 2019-02-27 15:50:08 -06:00
Ryan S. Elliott e95cf4e917 Some various doc updates for kim-api support 2019-02-14 13:38:28 -06:00
Ryan S. Elliott 333154633b Merge branch 'master' into kim-v2-update 2019-02-14 13:29:50 -06:00
Axel Kohlmeyer 9ac908f05f
switch download server for voro++ from LBL to download.lammps.org, which seems much more reliable 2019-02-13 09:53:20 -05:00
Stan Moore 773476634b Update Kokkos library in LAMMPS to v2.8.00 2019-02-08 08:50:26 -07:00
Ryan S. Elliott 927dc262b2 Update CMake & Install.py for KIM API v2 2019-02-06 23:41:45 -06:00
Ryan S. Elliott d677335b23 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-02-03 12:45:44 -06:00
Ryan S. Elliott a9b0fb9e9d Some adjustments to kim Install.py 2019-02-03 12:43:48 -06:00
Stan Moore 64834e4a3d Update Kokkos library 2019-02-01 12:45:54 -07:00
Axel Kohlmeyer 8ee1fefe19 add pointer to README and Manual to help. 2019-01-31 18:46:43 -05:00
Axel Kohlmeyer 763dda64af update lib/gpu/README to current state 2019-01-31 18:45:17 -05:00
Axel Kohlmeyer 1465352454 some cleanups and small bugfixes to conform better with python conventions 2019-01-28 17:37:05 -05:00
Axel Kohlmeyer 0cae619320 increase portability by using python modules instead of subprocesses 2019-01-28 15:54:19 -05:00
Axel Kohlmeyer b7ab017a76 improve portability by using shutil.copyfile, os.path.join, and make -C 2019-01-28 17:44:46 +01:00
Axel Kohlmeyer 4fcfa4987a fix typo 2019-01-28 14:56:47 +01:00
Axel Kohlmeyer 53f600ea35 use enable all available plumed modules when using download/compile mode 2019-01-26 09:55:48 -05:00
Axel Kohlmeyer 53673cd99c fix typo 2019-01-20 16:01:34 -05:00
Ryan S. Elliott 23ce00f366 Merge remote-tracking branch 'lammps/master' into kim-v2-update 2019-01-16 21:49:14 -06:00
Axel Kohlmeyer 683f8854c2 a few more Install.py script changes. untested. 2019-01-15 23:02:49 -05:00
Axel Kohlmeyer f8a8704ef4 use os.path.join(), os.symlink(), shutile.copyfile() and tarfile module 2019-01-15 18:07:50 -05:00
Axel Kohlmeyer 1ae112e563 small tweaks and improved consistency for Install.py in lib/kim 2019-01-14 18:03:32 -05:00
Axel Kohlmeyer cea0855fe4 small programming style cleanup 2019-01-14 17:47:58 -05:00
Axel Kohlmeyer d01c28002f update plumed support to use newer version of the library 2019-01-14 17:47:36 -05:00
Axel Kohlmeyer 54679b69f4 add argparse support to Install.py for kim library 2019-01-14 17:40:18 -05:00
Axel Kohlmeyer dc5385b290 add argparse support to Install.py in message lib 2019-01-14 17:13:46 -05:00
Axel Kohlmeyer 659bec582e update Install.py for LATTE to use the argparse module 2019-01-14 16:54:44 -05:00
Axel Kohlmeyer 2604b60eb8 properly apply version flag 2019-01-14 16:29:07 -05:00
Axel Kohlmeyer 718428df68 add md5 sum check for Voro++ download via Install.py 2019-01-14 15:03:29 -05:00
Axel Kohlmeyer 4eb141391b add md5 sum check for Eigen3 download via Install.py 2019-01-14 15:03:07 -05:00
Axel Kohlmeyer 23ad82a074 add md5sum check for ScaFaCoS download via Install.py 2019-01-14 15:02:38 -05:00
Axel Kohlmeyer ef25afcedb update Install.py for ScaFaCoS to use argparse 2019-01-14 14:44:32 -05:00
Axel Kohlmeyer e4cf409d69 update default Eigen3 version to the latest release 2019-01-14 14:13:53 -05:00
Axel Kohlmeyer c3a15e221d use sys.exit() instead of the removed error() function 2019-01-14 14:13:40 -05:00
Axel Kohlmeyer 59559f74e6 make smd/Eigen library Install.py script use argparse module 2019-01-14 13:55:22 -05:00
Axel Kohlmeyer 1e1f754d0c make gpu library Install.py use argparse module 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer 8d4bfa1aa7 port plumed and mscg Install.py files to use argparse 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer 3aacea671e use argparse in colvars lib build 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer 4e7329151d update generic Install.py script to use argparse 2019-01-14 12:52:21 -05:00
Axel Kohlmeyer aad8dd1462 use argparse for more consistent and robust argument parsing. 
this uses the code in PR #1244 as template. it supersedes the PR and thus closes #1244
 2019-01-14 12:52:21 -05:00
Ryan S. Elliott 6c0b100a53 Merge branch 'master' into kim-v2-update 2018-12-16 15:56:33 -06:00
Ryan S. Elliott b068690e13 Update for kim-api beta.3 release 2018-12-12 16:21:54 -06:00
Axel Kohlmeyer 02bdda0d05 Merge branch 'remove-reax-meam' into collected-post-stable-patches 2018-12-12 00:14:58 -05:00
Axel Kohlmeyer 0a610cb482 Merge branch 'sllod' into collected-post-stable-patches 2018-12-12 00:14:33 -05:00
Axel Kohlmeyer d15e4b1546
Merge branch 'master' into remove-reax-meam 2018-12-11 23:31:48 -05:00
Axel Kohlmeyer 8b5887bfb1 remove MEAM and REAX from lib folder 2018-12-10 12:05:29 -05:00
Axel Kohlmeyer fb08d3ea46 ignore MSCG build folder more generally 2018-12-10 11:25:24 -05:00
Axel Kohlmeyer 45b6b4bf52 Merge branch 'python-script-portability' into collected-post-stable-patches 2018-12-03 19:47:37 -05:00
Axel Kohlmeyer be721fe75a more Install.py refactoring 2018-12-03 19:47:10 -05:00
Axel Kohlmeyer 4168855ba3 reduce distracting nvcc (or rather ptxas) verbosity 2018-12-03 19:27:03 -05:00
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