5a341bee09
minor cleanup in docs and updated log files for kolmogorov/crespi/full
2018-03-23 06:42:04 -04:00
78e09e1854
refine the code and documentation
2018-03-23 13:26:40 +03:00
c398eb6b57
update kolmogorov-crespi examples
2018-03-22 19:42:07 -04:00
8de7c449fc
refactor code and examples to match LAMMPS conventions. whitespace cleanup. shorten examples.
2018-03-22 19:31:41 -04:00
04c968362f
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
6415befb5b
Add more examples
2018-03-14 16:30:54 +02:00
bbb2a6d641
Finally updated the github tutorial
2018-03-13 17:43:25 +02:00
375cf6124f
Finally updated the github tutorial
2018-03-13 17:27:23 +02:00
d9c6278844
Merge pull request #838 from zozo123/replaced-strcmpi-with-strncmpi-to-limit-number-of-chars-compared
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Tools/Matlab: Allow to read LAMMPS output fields
2018-03-12 16:39:35 -06:00
ce4ffe5933
Merge pull request #833 from stanmoore1/kk_update_2.6
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Update Kokkos library to v2.6.00
2018-03-12 13:51:33 -06:00
9c3296aad2
Tools/Matlab: Allow to read LAMPPS output field
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Some output fields have attributes attached on the same
line. e.g. "ITEM: BOX BOUNDS pp pp pp". This patch replaced all
the strcmpi to strncmpi in order to limit the number of character
compared with LAMPPS outputs.
Signed-off-by: Yossi Eliaz <eliaz123@gmail.com >
2018-03-12 13:45:13 -05:00
35abbab966
Merge pull request #835 from junghans/fix_python
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lammps.py: inconsistent use of tabs and spaces in indentation
2018-03-09 08:42:15 -07:00
d358e886c5
Merge pull request #834 from akohlmey/new-reax-logs
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provide new reference outputs for various reaxff examples
2018-03-09 08:41:44 -07:00
62d446668c
lammps.py: inconsistent use of tabs and spaces in indentation
2018-03-08 16:23:44 -07:00
fcfbdb13ab
provide new reference outputs for various reaxff examples
2018-03-08 18:10:28 -05:00
39786b1740
Update Kokkos library to r2.6.00
2018-03-08 10:57:08 -07:00
0c4c002f34
patch 8Mar18
2018-03-08 08:19:46 -07:00
bad1cdde78
Merge pull request #831 from lammps/mpi4py-version
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allow for mpi4py version 2 or 3 in Python wrapper
2018-03-07 14:01:22 -07:00
626ca25d05
Merge pull request #830 from akohlmey/more-fixes-for-stable
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More small fixes for stable release
2018-03-07 14:00:32 -07:00
a1bb877d55
correct commented out MPI examples
2018-03-07 11:17:03 -05:00
63c0a35fab
remove code that has no effect
2018-03-07 11:12:08 -05:00
812572ea97
update dependencies for colvars library
2018-03-07 10:57:56 -05:00
f91c36878c
remove dead code
2018-03-07 10:57:07 -05:00
fd1edaf04f
allow for mpi4py version 2 or 3 in Python wrapper
2018-03-07 08:52:46 -07:00
47e2ca6eb2
apply bugfix to reaxff taper function as described in issue #828
2018-03-07 09:52:14 -05:00
8d6fbd9829
Merge pull request #829 from lammps/restartinfo
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add restartinfo=0 to manbody file it was missing from
2018-03-06 15:17:05 -07:00
070e85b44b
add restartinfo=0 to manbody file it was missing from
2018-03-06 12:45:40 -07:00
3e535633e6
Merge pull request #827 from akohlmey/fixes-for-stable
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Fixes for stable release
2018-03-06 12:33:33 -07:00
64779eb576
documentation update for MEAM to clarify the I,J,K indices in the MEAM parameter file
2018-03-06 13:21:34 -05:00
1ca928b331
dead code removal
2018-03-05 20:33:19 -05:00
a1bdea1dd8
avoid division by zero for pair styles meam and meam/c
2018-03-05 14:03:10 -05:00
45555b017d
Merge pull request #728 from danicholson/cluster-fragment-aggregate-fixes
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Cluster/fragment/aggregate bugfixes
2018-03-02 15:52:26 -07:00
54f58faab5
Merge pull request #822 from andeplane/gcmc_mpi_error
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Added error if gcmc is used with molecules on more than one processor
2018-03-02 14:41:03 -07:00
22b6764304
Merge pull request #819 from stanmoore1/package_installed
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Add make package-installed command
2018-03-02 14:40:36 -07:00
39a09d3a54
Merge pull request #814 from stanmoore1/kk_snap_workaround
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Workaround issue in pair_snap_kokkos
2018-03-02 14:40:20 -07:00
812a45451a
Merge pull request #816 from giacomofiorin/colvars-update-2018-02-23
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Collected fixes and updates to Colvars library
2018-03-02 13:15:56 -07:00
0666607ceb
Merge pull request #815 from akohlmey/collected-small-fixes
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Collected small cleanups, fixes, and enhancements
2018-03-02 13:15:35 -07:00
d18ba3b188
Added error if gcmc is used with molecules on more than one processor
2018-03-02 11:23:34 -08:00
b1d3b56a17
apply bugfix reported in issue #820
2018-03-02 04:33:13 -05:00
8d0fdb17a6
Add make package-installed command
2018-03-01 10:39:06 -07:00
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
58e01a9eee
plug memory leak in pair style lj/class2/coul/long with coulomb tables
2018-02-25 14:03:07 +01:00
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
