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18048 Commits

Author SHA1 Message Date
Axel Kohlmeyer f9e34825f0
workaround for xcode oddity with compiling voro++ 2019-08-01 16:42:52 -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 de366c27e2
Merge pull request #1606 from oywg11/fix-ILP-bug 
Fix a communication bug of potential #839
 2019-08-01 15:01:13 -04:00
Axel Kohlmeyer 5fd323fe32
simplify example folder for ilp/graphene/hbn potential 
- flatten directory structure
- remove CPU time and reduce excess precision from output
- delete redundant and unused files
- regenerate reference outputs
 2019-08-01 14:24:47 -04:00
Axel Kohlmeyer 64b682b9f9
library compilation fix for clang with exceptions and -DLAMMPS_BIGBIG 2019-08-01 13:40:50 -04:00
Axel Kohlmeyer 083841ab2a
another compilation fix 2019-08-01 13:34:05 -04:00
Axel Kohlmeyer fa6a990536
reduce output precision to default and don't output per-step cpu time 2019-08-01 13:31:52 -04:00
Axel Kohlmeyer 73d2b824bd
fix compilation issue of library.cpp with exceptions enabled 2019-08-01 13:31:13 -04:00
Axel Kohlmeyer e17e6bb45d
Merge pull request #1605 from akohlmey/fix-compilation-errors 
Fix some compilation errors
 2019-08-01 11:24:30 -04:00
Axel Kohlmeyer 2fe4a6490c
restore include file cleanup changes 2019-08-01 11:20:06 -04:00
Axel Kohlmeyer 5fe457667e
restore showing references to potential files without pathnames 2019-08-01 11:19:39 -04:00
oywg11 02511a0ae5 Merge branch 'fix-compilation-errors' of https://github.com/akohlmey/lammps into fix-ILP-bug 2019-08-01 17:40:01 +03:00
oywg11 76bac4cedc Fix communication bug of ILP 2019-08-01 16:39:42 +03:00
oywg11 8f5cd8661f Fix communication bug of ILP 2019-08-01 16:38:19 +03:00
Michael Brown e57c3c04d0 Bug fixes for use of uninitialized variable and strict-aliasing in USER-INTEL. 2019-08-01 05:32:18 -07:00
Axel Kohlmeyer c967c09561
correct compilation error with exceptions enabled in main.cpp 2019-08-01 08:14:27 -04:00
Axel Kohlmeyer a6bd86eb77
make USER-OMP code compatible with pre-c++ 11 compilers again 2019-08-01 08:14:03 -04:00
Axel Kohlmeyer e3c91626c8
need to include update.h when exceptions are enabled 2019-08-01 07:07:21 -04:00
Axel Kohlmeyer 2a74832a1e
protect MPI library version detection from incompatible MPI libraries 2019-08-01 07:04:24 -04:00
Axel Kohlmeyer 86e3740fb3
use more common syntax for CPP's "defined" keyword 2019-08-01 07:03:51 -04:00
Axel Kohlmeyer 892e4759df
protect Spectrum MPI detection from failing to compile with MPI libraries implementing MPI version 2 or 1 2019-08-01 07:02:55 -04:00
Axel Kohlmeyer 207976f4e9
avoid abort when timeout appears in temper commands 2019-08-01 06:11:05 -04:00
Michael Brown 074ae06b36 Bug fix for eam/intel per-atom energy calculation. 2019-08-01 02:19:49 -07:00
Axel Kohlmeyer 75c1e28566
fix typo 2019-07-31 23:28:57 -04:00
Axel Kohlmeyer 58404946db
add timer timeout support to temper commands 2019-07-31 23:26:13 -04:00
Axel Kohlmeyer d09ca91627
Merge pull request #1599 from rbberger/collected-small-changes 
Collected small changes
 2019-07-31 19:13:41 -04:00
Axel Kohlmeyer e89cedbd99
Merge pull request #1601 from akohlmey/cmake-list-portability 
Improve compatibility to older CMake versions when building/installing LAMMPS library and headers
 2019-07-31 12:19:41 -04:00
Axel Kohlmeyer 4011f6650d
first step of adding timeout support to temper commands 2019-07-31 05:05:17 -04:00
Axel Kohlmeyer 0fa9cd5004
use utils::strmatch to simplify checks for compatible thermostat/barostat fixes 2019-07-31 05:03:59 -04:00
Richard Berger 3cc8508795 Add missing definition of NULL in USER-PTM header 2019-07-31 03:22:22 -04:00
Richard Berger da3b91a744 Remove not existing files from USER-PHONON Install.sh 2019-07-31 03:11:44 -04:00
Axel Kohlmeyer bc79412203
list(TRANSFORM ...) is not portable to older versions of cmake. work around it. 2019-07-30 22:54:02 -04:00
Axel Kohlmeyer 8803183b8b
Merge pull request #1593 from akohlmey/next_version 
Step version string for next patch release
 2019-07-30 22:25:26 -04:00
Axel Kohlmeyer 11a3fd6ce4
Merge pull request #1556 from lammps/bug-maxexchange 
more robust version of atom exchange size
 2019-07-30 17:09:18 -04:00
Axel Kohlmeyer e3b1673c8c
Merge pull request #1597 from stanmoore1/eff_be_test 
Fix failing regression test /examples/USER/eff/Be-solid/in.Be-solid.spe
 2019-07-30 17:07:55 -04:00
Axel Kohlmeyer 69a5ff2240
Merge pull request #1592 from akohlmey/collected-small-changes 
Collected small changes for next patch release
 2019-07-30 17:06:48 -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
Axel Kohlmeyer 528ec75f88
special case for MacOSX not needed 2019-07-30 16:38:40 -04:00
Axel Kohlmeyer f5bf86b32d
more improvements to CMake build for USER-PLUMED on MacOSX 
default to shared linkage on MacOSX to avoid linker issues from
configure/cmake library detection differences

link/depend on GSL and LAPACK explicitly only for static linkage
 2019-07-30 16:27:00 -04:00
Axel Kohlmeyer d4503a05a4
mention that cstdlib is included in lmptype.h now, too. 2019-07-30 14:22:33 -04:00
Axel Kohlmeyer 47fc31d005
move inline functions to the only place they are used. no need to use size_t for indices that are small 2019-07-30 14:21:53 -04:00
Axel Kohlmeyer 2d93a713e2
Merge branch 'master' into collected-small-changes 2019-07-30 14:14:11 -04:00
Axel Kohlmeyer 6d94fc1b3d
include cstdlib in lmptype.h since we define ATOX() macros. 2019-07-30 14:07:30 -04:00
Stan Moore 602b4a47c0 Fix failing regression test 2019-07-30 10:37:27 -06:00
Axel Kohlmeyer 8fa4efa08e
Merge pull request #1440 from ellio167/kim-simulator-models 
Develop native support for KIM simulator models
 2019-07-30 10:53:58 -04:00
Axel Kohlmeyer 3eadfa15ef
Merge pull request #1512 from mkanski/rotate_molecules 
Extend support of "rotate" keyword to all styles of "create_atoms"
 2019-07-30 10:53:37 -04:00
Stan Moore 3548551479 Fix Kokkos package compile error 2019-07-30 08:49:58 -06:00
Axel Kohlmeyer d1e8d7cbf8
Step version string for next patch release 2019-07-30 08:26:11 -04:00
Axel Kohlmeyer b0bccfd8a1
fix typo 2019-07-30 06:55:47 -04:00