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
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
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
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
63714c7079
remove PDF-only .txt file from Sphinx documentation processing
2018-02-13 13:10:20 +01:00
60f411d655
update manual content list for recent updates
2018-02-13 12:47:36 +01:00
7b551bb594
add a short command overview page for the PDF manual only
2018-02-13 12:47:05 +01:00
b0d8fb2170
promote header levels for better formatting in pdf manual
2018-02-13 12:43:56 +01:00
44faa8e9f5
insert new toplevel text into USER-ATC docs, change header levels.
2018-02-13 12:43:32 +01:00
3ceec36b84
improve format
2018-02-13 12:38:48 +01:00
f890cdfb9e
correct formatting in fix atc docs
2018-02-13 11:44:07 +01:00
3a909e15ae
remove non-functional doxygen generated navigation header from AtC doc files
2018-02-13 11:43:52 +01:00
7e78738c73
patch 5Feb18
2018-02-09 14:26:21 -07:00
3528f9ca27
fix bugs in documentation and implementation of atom style mdpd
2018-02-09 15:19:01 +01:00
49745968f2
make link unambiguous so sphinx is not confused
2018-02-06 16:57:27 +01:00
1d403b2aa3
Added warning to discourage use of group all and fixed some segfault cases
2018-02-05 13:29:14 -07:00
401bfc52e1
Merge pull request #798 from akohlmey/always-use-internal-xdr
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Replace OS provided XDR support with bundled code
2018-02-02 14:47:40 -07:00
7441b062e9
Merge pull request #792 from pastewka/18_dump_nc1
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Dumping to multiple files failed with an error message complaining about a missing 'append yes' option.
2018-02-02 14:45:52 -07:00
10d80ba9c3
Merge pull request #791 from akohlmey/charmm-cmap-docs-reference
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Update CMAP related docs and rebuild example input decks
2018-02-02 14:44:58 -07:00
e4a1826dee
Merge pull request #783 from numericalfreedom/lammps-doxygen
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Added double quotes to a word in Section_tools.txt file
2018-02-02 14:41:56 -07:00
160edc9532
Merge pull request #782 from hheenen/user-mofff-contribution
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User mofff contribution
2018-02-02 14:41:28 -07:00
553b3ff69a
Merge pull request #778 from athomps/fix_gcmc_segfault_fix
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Fixed recent segfault in fix gcmc and added mcmoves keyword
2018-02-02 14:40:14 -07:00
4af14becb5
Merge pull request #710 from rpleite/add-pair-ufm
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Add the UFM pair potential - (GPU/OPT/OMP)
2018-02-02 14:38:28 -07:00
85fdf9eaba
make links to papers unique across files
2018-02-02 10:10:27 +01:00
2ff278defa
fully integrate ufm into documentation
2018-02-02 10:02:44 +01:00
c3d1cee5f9
try to use OS-provided (and obsoleted) RPC headers for XDR. always use bundled code
2018-02-02 09:23:02 +01:00
b70149e86a
include added docpages in toctrees for sphinx
2018-02-01 18:50:25 +01:00
080ce422ae
correct incorrect reference
2018-02-01 18:40:28 +01:00
cc54848f7b
adapt to current manual conventions
2018-02-01 18:40:17 +01:00
9cf4ac8b7c
DOC: Added netcdf and netcdf/mpiio to dump style supporting atom attributes.
2018-01-28 14:24:28 +01:00
cf8dae5ef3
explain position of fix cmap command in input for data and restart files
2018-01-28 06:20:03 -05:00
ba68548e38
clarify ch2lmp commands purpose in tools section
2018-01-28 06:19:33 -05:00
