d3169eeab3
Remove Make.py reference in PyLammps examples
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Also fixes some regressions due to command syntax changes
2017-07-31 13:56:20 -06:00
71553cf732
Fix PyLammps regression after output.cpp change
2017-07-31 13:53:41 -06:00
6d0a228624
Merge pull request #599 from lammps/kim-doc
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restore lost KIM doc section in Section packages
2017-07-27 10:34:44 -06:00
934cbbbeca
restore lost KIM doc section in Section packages
2017-07-26 16:07:08 -06:00
2806f070a4
Merge pull request #598 from akohlmey/last-minute-changes
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last minute changes for stable release
2017-07-26 15:46:51 -06:00
f7a243a4d9
convert explicit copies back into symbolic links
2017-07-26 14:20:03 -04:00
f0d286358e
must not include system headers within 'extern "C"' blocks. breaks with MPICH
2017-07-26 14:02:02 -04:00
51a06334ad
avoid invalid calls to memcpy(): when ndot == 0, pointers may be NULL
2017-07-26 12:08:42 -04:00
aa5ea95a0f
avoid integer overflow and remove unused function argument causing it
2017-07-26 11:55:50 -04:00
60c67b07dc
import updated fix msst file with some additional cleanup and simplification
2017-07-26 10:45:11 -04:00
a59b7e4d56
patch 24Jul17
2017-07-24 09:09:22 -06:00
2eaea2d274
Merge pull request #594 from junghans/license
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LICENSE: update address of Free Software Foundation
2017-07-24 08:56:11 -06:00
1ddace4dba
Merge pull request #595 from libAtoms/idces2quip
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Add a (contrived) molecular example for USER-QUIP
2017-07-24 08:55:03 -06:00
af3d0ca381
Merge pull request #593 from akohlmey/collected-bug-fixes-and-small-updates
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Collected bug fixes and small updates
2017-07-24 08:54:16 -06:00
c24e316baa
avoid floating point overflows in iterative solvers of fix shake
2017-07-22 23:15:01 -04:00
2c6e177d5c
avoid reporting negative memory allocation when memory_usage() is called before initialized
2017-07-22 23:14:17 -04:00
7b2182833f
disallow binary output with dump style local. fixes #596
2017-07-22 10:35:16 -04:00
1afab981b0
Clarified some points in in.molecular example
2017-07-22 14:40:33 +01:00
1af937e99d
Update in.molecular
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- expand comments to provide more details on the choice of exclusion settings
- comment out dump file generation
2017-07-21 22:00:29 -04:00
4e0a249e27
Add a (contrived) molecular example for USER-QUIP
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This example showcases the use of different 'special_bonds' settings for
different pair styles, so quip gets all the bonded neighbours but lj can
exclude them if it needs to.
The results have been checked against a pure quip implementation of the
potential; the expected lammps output is included.
DISCLAIMER: This example mixes parameters for methane and silane and is
NOT intended to be a realistic representation of either system.
2017-07-22 01:33:15 +01:00
edc756a65f
LICENSE: update address of Free Software Foundation
2017-07-21 17:13:28 -06:00
a477f26477
add support for trapping floating point exception as an optional compile time feature
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we may make this a run time setting by connecting this code to a command.
2017-07-21 15:37:40 -04:00
b1b399d5c3
update readme for examples
2017-07-21 15:06:15 -04:00
00474ab09d
handle one more case where allowing shifted potential with cutoff 0.0 would create NaNs
2017-07-21 10:30:11 -04:00
733ea61bf1
correct typo in USER-REAXC code
2017-07-21 01:15:24 -04:00
5c13b087e4
Merge pull request #592 from akohlmey/reaxc-bugfix
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Bugfix for USER-REAXC and reaxc in KOKKOS and USER-OMP
2017-07-20 16:26:20 -06:00
ec23aef20b
fix reaxc division by zero bug also for USER-OMP variant
2017-07-20 18:19:53 -04:00
61b1487cbd
avoid division by zero in reaxff bond interaction computations in very rare cases
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this addresses the issue reported by stan and ishan
2017-07-20 18:17:19 -04:00
e53583d9c6
Merge pull request #590 from lammps/fortran-dftb
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update of Fortran-DFTB interface to be compatible with fix msst
2017-07-20 15:30:23 -06:00
551001f172
revert change, that is part of the kim-install branch and changeset
2017-07-20 17:08:19 -04:00
5dbe2df854
revert change that accidentally undoes part of PRs #583 and #588
2017-07-20 17:07:31 -04:00
3f83396837
Merge pull request #588 from akohlmey/colvars-quickfix
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avoid makefile failure, if LAMMPS has not been configured yet
2017-07-20 14:45:25 -06:00
59db5f6a17
update of Fortran-DFTB interface to be compatible with fix msst
2017-07-20 14:40:35 -06:00
1b704bab18
Merge branch 'colvars-safer-makefiles' of https://github.com/giacomofiorin/lammps into colvars-quickfix
2017-07-20 15:59:23 -04:00
c98f6140e7
Change order of targets in Makefiles for Colvars
2017-07-20 15:49:31 -04:00
5031f5b807
Comment out use by Colvars of Makefile.lammps from other packages
2017-07-20 15:48:10 -04:00
9d0d90c038
README clarification from giacomo
2017-07-20 15:25:27 -04:00
66154e8a8b
avoid makefile failure, if LAMMPS has not been configured yet
2017-07-20 15:05:58 -04:00
3cd597e948
Merge pull request #585 from akohlmey/make-py-manual-cleanup
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Make.py removal and manual cleanup
2017-07-20 12:05:04 -06:00
eca61226c2
Merge pull request #583 from giacomofiorin/colvars-update-2017-07-19
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Update Colvars to version 2017-07-15 and support automated builds for it
2017-07-20 12:04:49 -06:00
fac3e3daa2
Merge pull request #581 from libAtoms/idces2quip
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Modified USER-QUIP interface to pass lammps atom IDs
2017-07-20 12:04:32 -06:00
72e5f537c8
Merge pull request #576 from akohlmey/sanitizer-changes
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Collected changes for issues detected by gcc -fsanitize
2017-07-20 12:03:40 -06:00
bdd2f3a6b2
remove references to Make.py and USER-CUDA
2017-07-20 12:25:42 -04:00
a351977c59
update manual links that got broken when removing and renumbering a section
2017-07-20 12:25:42 -04:00
8499e72cdc
updates to USER-REAXC code in USER-OMP from Chris Knight. addresses issues with multiple threads in use
2017-07-20 12:11:46 -04:00
ef9fb944c7
Detect number of processors for make
2017-07-20 10:53:08 -04:00
187a80be77
Add forgotten decode() in Install.py
2017-07-19 22:21:49 -04:00
ee6cac826e
Update Colvars to version 2017-07-15 and support automated builds for it
2017-07-19 14:24:07 -04:00
52a1c54d50
support QUIP wrapper API version query, relax hybrid restriction to allow hybrid/overlay, update docs
2017-07-19 13:17:35 -04:00
fcf9607a66
Update USER_QUIP docs to clarify use of "special_bonds"
2017-07-19 17:47:21 +01:00
