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14513 Commits

Author SHA1 Message Date
Axel Kohlmeyer b11757adb3 replace variable length array in fix ipi with new/delete 2018-05-04 16:47:29 -04:00
Axel Kohlmeyer b61834f28d replace variable length array with fixed size 2018-05-04 16:34:46 -04:00
Axel Kohlmeyer 1d54c93df8 replace variable length array with new/delete in PNG support of dump image 2018-05-04 16:30:52 -04:00
Axel Kohlmeyer 330f29db0b replace variable length arrays in USER-PHONON with new/delete 2018-05-04 16:26:48 -04:00
Axel Kohlmeyer 366aaf2450 port bugfix for single/bond to single/angle and single/dihedral 2018-05-04 00:32:13 -04:00
Axel Kohlmeyer c9d41178d8 update logfiles and adjust some example inputs to be consistent 2018-05-03 23:37:01 -04:00
Axel Kohlmeyer 6886dcb2e4 correct minor issues, so LAMMPS compiles again 2018-05-03 23:04:07 -04:00
Axel Kohlmeyer 23f71ee4ad fix bug in create_bonds, where ghost atoms were counted incorrectly 2018-05-03 22:34:11 -04:00
Steven J. Plimpton 844858d3a7 2nd set of updates 2018-05-03 17:00:08 -06:00
Steven J. Plimpton 2b8576c7c7 first updates 2018-05-03 16:55:22 -06:00
Steve Plimpton eeee2d3026
Merge pull request #803 from jrgissing/fix_bond_react 
Fix bond react
 2018-05-03 14:16:46 -06:00
Axel Kohlmeyer 53cc609c4c make filenames comply with LAMMPS conventions and add reference log files 2018-05-03 16:03:37 -04:00
Axel Kohlmeyer c8a0689d78 correct typo in converting c-library header includes to c++ styles 2018-05-03 15:44:17 -04:00
Steven J. Plimpton 28786ef99b tweak to header file names 2018-05-03 11:49:27 -06:00
Steve Plimpton 749f1ff407
Merge pull request #875 from akohlmey/collected-small-fixes 
Collected small changes and bug fixes for the next patch release
 2018-05-03 11:28:00 -06:00
Steve Plimpton 654fec164d
Merge pull request #881 from akohlmey/cplus-plus-style-includes 
Replace C-style include files with their C++ equivalents
 2018-05-03 11:25:51 -06:00
Steve Plimpton 35294dafbc
Merge pull request #883 from giacomofiorin/colvars-update 
Fixes to Colvars library (version 2018-04-29)
 2018-05-03 11:25:32 -06:00
Steve Plimpton 83f5c331cd
Merge pull request #886 from lammps/snap-quadratic 
updates to quadratic form of SNAP potential
 2018-05-03 11:21:29 -06:00
Axel Kohlmeyer 1fdb010c41 Revert "workaround for ISFINITE() macro to work with the latest KOKKOS library update" 
This reverts commit f202f1bcf6.
 2018-05-03 13:08:15 -04:00
Axel Kohlmeyer b5b70b429f update log files for SNAP package examples to reflect current state of keywords. 2018-05-03 13:00:24 -04:00
Axel Kohlmeyer 07a15a719f whitespace cleanup 2018-05-03 12:38:24 -04:00
Steven J. Plimpton 75cffc78c5 updates to quadratic form of SNAP potential 2018-05-03 10:23:50 -06:00
Giacomo Fiorin 0c005f5cb0 Small fixes to Colvars library 
Primarily a list of small fixes, combined with cosmetic changes and cleanups
in several files.

6d0c917 2018-04-29 Fix missing deallocation of output stream object (reported by HanatoK) [Giacomo Fiorin]
c92d369 2018-04-17 Do not test for atom group size [Jérôme Hénin]
431e52a 2018-04-06 Allow scripted/custom colvars to be periodic [Jérôme Hénin]
81d391f 2018-04-05 Split colvarcomp constructor into POD constructor + init() function [Giacomo Fiorin]
9b85d5f 2018-03-13 Fix issue with out-of-order atom selections; clarify format for ref positions [Giacomo Fiorin]
0e0ed37 2018-03-07 Support triclinic unit cells in VMD, clean up PBC functions [Giacomo Fiorin]
eed97c9 2018-02-24 Obtain integer version number from version string [Giacomo Fiorin]
c17f3cd 2018-02-23 Write trajectory labels only when needed [Giacomo Fiorin]
 2018-05-02 15:03:56 -04:00
Michael DeLyser fc0110a2e0
Update fix_bocs.cpp 2018-05-02 13:25:26 -04:00
Michael DeLyser 072a063afc
Delete fix_bocs.html 2018-05-02 11:30:25 -04:00
Michael DeLyser fbf96b680b
Delete MOD_COMPUTE_H 2018-05-02 11:29:41 -04:00
Michael DeLyser ed3f8d4b3f
Update methanol.lmp 2018-05-02 11:28:44 -04:00
Michael DeLyser efbee4a292
Delete man_fix_bocs.html 2018-05-02 11:27:31 -04:00
MICHAEL ROBERT DELYSER 2e2f19770c Removed .html files. Removed compute.h mods. Cast pressure for functions 2018-05-02 11:14:30 -04:00
Axel Kohlmeyer 25ac1fd16c mention that fix reax/bonds and reax/c/bonds do not honor the group id 2018-05-01 18:55:00 -04:00
Axel Kohlmeyer ca6f99129d revert <cinttypes> back to <inttypes.h> as the former seems to require C++-11 2018-04-27 18:39:11 -04:00
Axel Kohlmeyer 0015b15b18 revert <cstdint> back to <stdint.h> as the former seems to require C++-11 2018-04-27 18:25:30 -04:00
Axel Kohlmeyer e4071d7f46 replace C-style include files with their C++ equivalents 2018-04-27 18:00:24 -04:00
Stan Moore 6b92826a1a Remove Kokkos deprecated code 2018-04-27 12:35:00 -06:00
Axel Kohlmeyer f202f1bcf6 workaround for ISFINITE() macro to work with the latest KOKKOS library update 2018-04-27 14:15:32 -04:00
Axel Kohlmeyer 64b08d3ca8 add write_data() support to remaining improper styles. 
with this commit, write_data() support should be complete.
 2018-04-26 16:39:31 -04:00
Axel Kohlmeyer c7edc6636a make sure all allocatable class pointers are initialized to NULL 2018-04-26 16:13:19 -04:00
Michael DeLyser 56d0014a4a
Added #include "citeme.h" 2018-04-26 10:05:49 -04:00
Axel Kohlmeyer 26d22a4b7a restrain energy must be incremented. bugfix from robert meissner posted to lammps-users 2018-04-26 10:02:42 -04:00
MICHAEL ROBERT DELYSER c5e884fb41 USER-BOCS 2018-04-26 09:34:47 -04:00
jrgissing c4373c7afa add extract to fix_group 
this will allow users to define groups that are by default created internally by fixes, etc.
 2018-04-24 22:53:54 -06:00
Jacob Gissinger 69665c218a
Merge pull request #9 from lammps/master 
rebase
 2018-04-24 22:09:17 -06:00
Axel Kohlmeyer 6f9a2245d2 add write_data() support to 4 more dihedral styles, which completes the set 2018-04-23 16:56:19 -04:00
Steven J. Plimpton d5ec76290b patch 20Apr18 2018-04-20 17:22:38 -06:00
Steve Plimpton 836027dbd8
Merge pull request #867 from stanmoore1/kk_tweaks 
Tweaks to KOKKOS package
 2018-04-20 14:35:58 -06:00
Steve Plimpton c5127eca89
Merge pull request #872 from akohlmey/ave-correlate-long-bugfix 
Bugfix for fix ave/correlate/long
 2018-04-20 09:30:02 -06:00
jrgissing 91b407570a docfix 
remove mention of as yet unreleased feature
 2018-04-19 20:23:58 -06:00
Axel Kohlmeyer 5bf8e1bc5b add ability to retrieve the number of local rows for computes returning local data 
this is done supporting the combination of type == 2 with style == 0,
i.e. a local scalar, which is not available in C++ (but there one can
access the compute style data member directly. for the python interface,
the pointer is automatically dereferenced and returned as a c_int.
 2018-04-19 18:37:15 -04:00
Axel Kohlmeyer 164537cf37 whitespace cleanup 2018-04-19 18:30:51 -04:00
Axel Kohlmeyer f1ee46cc64 add check to require atom attribute molecule to avoid segfaults, when it is missing 2018-04-19 18:24:19 -04:00