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4364 Commits

Author SHA1 Message Date
Steve Plimpton 03a7d1cd5d
Merge pull request #933 from rtoijala/fix_dt_reset_energy 
Limit atom energy change in fix dt/reset
 2018-06-18 13:43:03 -06:00
Steve Plimpton 08331da93d
Merge pull request #950 from martok/subst-equal-fmt 
Add support for inline format strings to immediate variable substitution
 2018-06-18 13:42:24 -06:00
Steve Plimpton ab0f3debeb
Merge pull request #948 from martok/variable-string 
Variable style 'string' substitutes variables in definition
 2018-06-18 10:50:36 -06:00
Axel Kohlmeyer c4bcb7e73d mention requirement to come after the box creation in Restrictions section 2018-06-15 17:52:54 -04:00
Axel Kohlmeyer 18b543179c fix typo 2018-06-15 17:47:23 -04:00
Axel Kohlmeyer 14c4438a72 update docs to reflect the state of reserving space for topology info with molecule files 2018-06-15 17:46:09 -04:00
Axel Kohlmeyer 5fcdfe6dcb describe the use of wildcards for adapting ranges of bond types 2018-06-15 17:35:43 -04:00
Sebastian Hütter c5b51df06e Add support for inline format strings to immediate variable substitution 2018-06-14 14:17:37 +02:00
Sebastian Hütter 3e79296dcf Variable style 'string' substitutes variables in definition 2018-06-14 13:10:08 +02:00
Axel Kohlmeyer 56c3a0be29 support virtualenv on machines with python3 where it is called virtualenv-3 2018-05-31 19:03:28 -04:00
Axel Kohlmeyer cf3095e938 document restartinfo bug message, add check to Pair::write_restart as well 2018-05-31 19:02:03 -04:00
Axel Kohlmeyer 38182dcc60
clarify docs on what energy is monitored 
changes to the energy only consider the kinetic energy, so make that explicit in the augmented `fix dt/reset` docs
 2018-05-31 17:32:19 -04:00
Risto Toijala b9a8f91753 Limit atom energy change in fix dt/reset 
Allow limiting of the maximum energy change of an atom in
fix dt/reset in addition to the existing distance limit.
Useful especially for high-energy irradiation.
 2018-05-28 10:57:40 +03:00
Steven J. Plimpton cab602045e tweaks to doc pages 2018-05-18 08:37:29 -06:00
jrgissing 363d8ef775 tweaks1 2018-05-13 15:45:43 -06:00
jrgissing a449488b1d simplify 2018-05-13 12:14:15 -06:00
jrgissing e076d08ee9 correctly render doc page 2018-05-12 14:17:29 -06:00
Steve Plimpton ca6920be72
Merge pull request #907 from akohlmey/dump_maxfile 
Implement 'dump_modify maxfiles' feature
 2018-05-12 12:59:33 -06:00
Steven J. Plimpton 0f32d603b5 tweaks to dump_modify maxfiles doc page 2018-05-11 15:52:18 -06:00
Steve Plimpton 3440b1a2a7
Merge pull request #909 from lammps/tablecut 
new dihedral table/cut command
 2018-05-11 15:41:52 -06:00
Axel Kohlmeyer 4d34e55072 rename jpeg file, recreate tex file and fix typo in docs for dihedral style table/cut 2018-05-11 17:31:14 -04:00
Axel Kohlmeyer 821ef0cf77 update documentation for dihedral style table/cut 2018-05-11 16:08:23 -04:00
Steven J. Plimpton 8d24101df4 patch 11May18 2018-05-11 14:04:49 -06:00
Steven J. Plimpton 9674512997 new dihedral table/cut command 2018-05-11 07:36:40 -06:00
Axel Kohlmeyer 7780d92823 implement 'dump_modify maxfiles' feature as discussed 2018-05-10 23:25:26 -04:00
Axel Kohlmeyer 671876efef
Make the description of global properties more explicit 2018-05-08 15:33:42 -04:00
robeme 53fc9f1f0f updated doc for new fix restrain output 2018-05-08 10:11:00 +02:00
Steve Plimpton a4759210a8
Merge pull request #893 from ohenrich/user-cgdna 
Docs update and journal reference for USER-CGDNA package
 2018-05-07 14:39:32 -06:00
Steve Plimpton 7fed6c7e4c
Merge pull request #634 from craabreu/master 
Computation of forces/torques on rigid bodies moved to post_force
 2018-05-07 14:39:10 -06:00
Axel Kohlmeyer 7cf42e42eb
make links to citations unique across files 2/2 2018-05-07 14:25:18 -04:00
Axel Kohlmeyer d80b375e26
make links to citations unique across files 1/2 2018-05-07 14:24:00 -04:00
Oliver Henrich 5076b6d161 Removed old documentation 2018-05-07 18:25:55 +01:00
Oliver Henrich fcdcdb3286 Merge branch 'master' into user-cgdna 2018-05-07 18:19:24 +01:00
Oliver Henrich 722549965e Added reference to implementation paper 2018-05-07 18:13:18 +01:00
Steve Plimpton ca96a7ab05
Merge pull request #891 from akohlmey/collected-small-changes 
Collected small changes, fixes and updates
 2018-05-07 10:43:19 -06:00
Steve Plimpton a7c9418629
Merge pull request #890 from jrgissing/bond_react_final_touches 
bond/react final touches
 2018-05-07 10:37:47 -06:00
Axel Kohlmeyer d9d33ac766 add ability to set multiplicity for dihedrals with fix restrain 
this introduces an optional keyword, so backward compatibility is preserved.
this closes #884
 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer d51745fd27 whitespace cleanup 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer c3588f08b7 provide keyword/value option to compute ackland/atom for selecting legacy or current variant of implementation 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer ecfe5c8373 use american spelling of neighbor consistently in docs and code comments 2018-05-07 07:23:29 -04:00
Axel Kohlmeyer 5e49976b70 correct typo in fix bond/react docs 2018-05-06 11:17:34 -04:00
jrgissing 916ed71760 fix bond/react final touches 2018-05-06 00:34:03 -06:00
Axel Kohlmeyer 735bceb468 Merge branch 'master' into USER-BOCS 2018-05-05 10:21:21 -04:00
Axel Kohlmeyer 81293b0fda changes to integrate USER-BOCS into LAMMPS and to closer follow the LAMMPS programming/documentation style 2018-05-05 10:21:11 -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
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 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
Steven J. Plimpton 75cffc78c5 updates to quadratic form of SNAP potential 2018-05-03 10:23:50 -06:00