eadac15466
avoid multiple calls to delete [] on the same pointer.
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thanks to @ExHP for pointing out this issue
2018-02-28 14:02:16 +01:00
51b19dfd1a
plug memory leak in fix bond/react
2018-02-25 14:10:28 +01:00
58e01a9eee
plug memory leak in pair style lj/class2/coul/long with coulomb tables
2018-02-25 14:03:07 +01:00
3b90f60064
Merge pull request #3 from lammps/master
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rebase
2018-02-24 23:49:27 -07:00
7d1de34533
gatherv fix, doc updates
2018-02-24 22:49:28 -07:00
5fb2979da7
allow dynamic groups for some standard walls interacting with point particles
2018-02-24 13:50:42 -05:00
948f4783aa
ring communication *is* called with outbut set to NULL, so don't error out on that.
2018-02-24 17:17:45 +01:00
fb6e7e8aea
add sanity checks for ring communication
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we do not call memcpy() unless nbytes != 0 and source/target pointer is not NULL
we error out on illegal combinations of nbytes and inbuf/outbuf
2018-02-24 16:41:10 +01:00
bba4bd1489
support offsets for molecule IDs (if available) in read_data similar to atomIDs
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suggested by felipe perez in https://sourceforge.net/p/lammps/mailman/message/36236631/
2018-02-23 18:02:05 -05:00
4a875dc67d
Workaround for compiler bug in gcc v4.9.3, manifest in KOKKOS SNAP
2018-02-23 09:01:34 -07:00
f3cf407a21
Collected fixes and updates to Colvars library
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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
0003bb6766
merge capture regions, so the library interface code can compiled with exceptions
2018-02-23 14:20:39 +01:00
523978b4c7
dead code and uninitialized variables detected by clang
2018-02-23 12:04:15 +01:00
d5e43a9ab1
whitespace cleanup and reindent
2018-02-23 10:20:29 +01:00
939b1b2d05
Workaround issue in pair_snap_kokkos_impl
2018-02-22 14:27:23 -07:00
77efd3dfb3
Merge pull request #813 from akohlmey/correct-neighbor-build
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Make default argument for virtual method Neighbor::build() explicit
2018-02-22 08:48:06 -07:00
feb9f29fad
Merge pull request #812 from akohlmey/correct-integrate-setup
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Make default argument for pure method Integrate::setup() explicit
2018-02-22 08:47:45 -07:00
bfdf464ee3
patch 22Feb18
2018-02-22 08:46:03 -07:00
99d5957a01
make default argument of virtual function Neighbor::build() explicit
2018-02-22 08:42:36 -05:00
65acd233ce
forgot to remove one default argument on a method derived from Integrate::setup()
2018-02-22 08:13:54 -05:00
cf3887c5e0
default arguments on polymorph/pure methods can lead to unexpected overloading in derived classes
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argument for Integrate::setup() made explicit
2018-02-22 07:53:58 -05:00
3787b89447
re-add compressed data file (was hidden by .gitignore)
2018-02-22 02:31:25 -05:00
8fef7880e7
dead code removal and loop construct fixes to silence compiler warnings.
2018-02-22 02:23:57 -05:00
a8eb3ff77f
consolidate per-atom property fixes into one
2018-02-21 23:20:17 -07:00
e1d1c87656
Merge pull request #811 from akohlmey/check-latte-version
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Tiny update to fix latte for checking library version
2018-02-21 10:54:58 -07:00
bcef43c7d1
add code to check the ABI version of the LATTE library
2018-02-21 12:11:02 -05:00
aa1503b7e0
Merge pull request #800 from athomps/fix_gcmc_segfault_fix
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Added warning to discourage use of group all and fixed some segfault …
2018-02-21 09:50:22 -07:00
d9d072df65
Merge pull request #809 from Jc11235/fix_neb_old_tangent_implementation
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added old tangent to fix_neb for AGNI potential
2018-02-21 09:49:39 -07:00
a3cd600052
Merge pull request #786 from jrgissing/per_atom_prop_group
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per-atom property dynamic group
2018-02-21 09:48:49 -07:00
53fb7f4015
Merge pull request #810 from lammps/latte-error2
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2nd try on LATTE error returns, plus a couple minor doc edits
2018-02-21 09:47:17 -07:00
38ce56f252
fix documentation issues: non-ASCII characters, broken/missing links, formatting
2018-02-21 11:53:18 +01:00
5191071581
no need to cast fixes to specific styles/types
2018-02-21 11:15:44 +01:00
b6821ed942
since the code uses static ids, only one instance is allowed at a time
2018-02-21 11:15:09 +01:00
deeba53a24
consolidate inclusion file style with LAMMPS conventions
2018-02-21 11:14:32 +01:00
daae906162
move fix bond/react examples and compress large data file
2018-02-21 10:30:35 +01:00
b252866393
sync fix temp/rescale to upstream
2018-02-21 10:17:00 +01:00
a672874186
Update comment
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Clarify the comment as to why this else branch was added and what this represents.
2018-02-21 10:04:13 +01:00
911529ab24
correct typo
2018-02-21 08:43:33 +01:00
a5a47899a3
make XDR support for dump style xtc compile on MacOSX
2018-02-20 22:10:21 +01:00
c399b75dec
2nd try on LATTE error returns, plus a couple minor doc edits
2018-02-20 12:52:12 -07:00
9cf99ef479
Merge pull request #806 from vishalkenchan/new_pair_lj_cut_coul_wolf
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Lennard-Jones with Coulomb interactions accounted through Wolf sum
2018-02-20 11:55:37 -07:00
54740a0668
Merge pull request #804 from akohlmey/collected-small-changes
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Collected small changes for next patch release
2018-02-20 11:54:24 -07:00
9f7b837f34
replace non-ASCII character
2018-02-20 17:18:56 +01:00
a8a38216ae
added old tangent to fix_neb for AGNI potential
2018-02-20 10:06:24 -05:00
54dc73c771
correctly compute adjusted box lengths for triclinic boxes. code taken from topotools
2018-02-19 14:06:26 +01:00
7bd089aa6d
fix typo
2018-02-19 14:05:50 +01:00
d52c5435a7
ignore installed copy of fix bond/react
2018-02-18 17:12:03 +01:00
75a432833b
remove messy hack
2018-02-18 17:11:06 +01:00
5843be1557
move fix bond/react to USER-MISC package
2018-02-18 17:03:40 +01:00
7ec4a5818d
add USER-OMP versions of lj/cut/coul/wolf
2018-02-18 16:38:50 +01:00
