7786cb5a4b
patch 30Mar18
2018-03-30 15:21:55 -06:00
a19e8fb269
Merge branch 'master' into resetids
2018-03-30 09:15:24 -06:00
81caeffb38
Merge pull request #855 from lammps/dumpinc
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new dump_modify refresh and compute displace/atom refresh commands fo…
2018-03-30 09:07:19 -06:00
a4795df5f9
complete integration of reset_ids into the documentation build system
2018-03-30 10:49:38 -04:00
ef8423918a
fix typo
2018-03-29 17:04:53 -04:00
09313cf3b5
shift files into doc/src
2018-03-28 13:35:13 -06:00
a524d8c193
Merge pull request #854 from lammps/readdump
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new option *add keep* added to read_dump
2018-03-27 14:39:35 -06:00
b571f5423a
Merge pull request #850 from lammps/addlib
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a few new lib interface methods
2018-03-27 14:39:16 -06:00
2aef3a0e96
new dump_modify refresh and compute displace/atom refresh commands for incremental dump files
2018-03-27 14:37:04 -06:00
e8b8428f6b
new option *add keep* added to read_dump
2018-03-27 10:08:58 -06:00
1956d93af9
doc tweak on added lib functions
2018-03-27 09:58:53 -06:00
f38169f19c
do not capitalize library.cpp, even if it is at the beginning of a sentence
2018-03-23 16:08:40 -04:00
5770a59ead
Merge pull request #846 from akohlmey/pdf-manual-reorg
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Refactor PDF Manual Structure
2018-03-23 13:40:35 -06:00
318877ada3
Merge pull request #839 from oywg11/master
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New registry dependent interlayer potential in LAMMPS
2018-03-23 13:38:48 -06:00
d14c16a47c
a few new lib interface methods
2018-03-23 13:34:22 -06:00
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
04c968362f
fix up and integrate documentation for contributed pair styles
2018-03-22 18:20:19 -04:00
1a402d4002
refactor headline levels to result in a more structured PDF manual
2018-03-20 15:42:13 -04:00
f6c76e04b8
patch 16Mar18
2018-03-19 08:26:58 -06:00
6415befb5b
Add more examples
2018-03-14 16:30:54 +02:00
375cf6124f
Finally updated the github tutorial
2018-03-13 17:27:23 +02:00
0c4c002f34
patch 8Mar18
2018-03-08 08:19:46 -07:00
070e85b44b
add restartinfo=0 to manbody file it was missing from
2018-03-06 12:45:40 -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
959883ad03
rename noextra option to nofix
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since this corresponds to the `fix` option of `read_data`, calling this flag `nofix` seems more consistent and descriptive.
2018-03-04 09:49:50 -05:00
a323147819
noextra option for write_data
2018-03-03 14:28:35 -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
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
8d0fdb17a6
Add make package-installed command
2018-03-01 10:39:06 -07:00
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
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
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
bfdf464ee3
patch 22Feb18
2018-02-22 08:46:03 -07:00
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
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
38ce56f252
fix documentation issues: non-ASCII characters, broken/missing links, formatting
2018-02-21 11:53:18 +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
7ec4a5818d
add USER-OMP versions of lj/cut/coul/wolf
2018-02-18 16:38:50 +01:00
65870843a5
fix typo in stride2() description in variable command docs reported by Jerome Guterl
2018-02-18 15:37:35 +01:00
c864e55adb
Lennard-Jones potential with Coulomb interactions accounted through Wolf summations
2018-02-18 14:20:59 +01:00
3d12cff8a5
Merge branch 'patch-1' of https://github.com/evoyiatzis/lammps into collected-small-changes
2018-02-16 10:55:25 +01:00
a30ede80a6
avoid triggering misformatting of manual overview table with txt2html
2018-02-15 12:12:19 +01:00
2aa693c46c
update authors list and packages from http://lammps.sandia.gov/authors.html
2018-02-15 05:06:54 -05:00
69f813b22e
fix up formatting of tutorials for PDF manual
2018-02-13 16:41:23 +01:00
b3693f891b
different style of AtC page headers that works well with html and pdf
2018-02-13 16:40:50 +01:00
1a213363f1
add group style to create an empty group directly
2018-02-13 14:54:30 +01:00
60f411d655
update manual content list for recent updates
2018-02-13 12:47:36 +01:00
