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File lammps.changes of Package lammps (Revision 1737c667ccc13d85323240df796daaa1)

Currently displaying revision 1737c667ccc13d85323240df796daaa1 , Show latest

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Sun Jun 14 20:44:26 UTC 2020 - Christoph Junghans <junghans@votca.org>

- disable march=native optimization by setting empty 
  CMAKE_TUNE_FLAGS

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Wed May 13 13:42:58 UTC 2020 - Christoph Junghans <junghans@votca.org>

- fix build on ppc64le by enabling gnu extensions, see
  [gh#lammps/lammps#2079], this is a bug in older version of the
  ocl package, compare [GCC#58241].

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Sun May 10 16:59:26 UTC 2020 - Christoph Junghans <junghans@votca.org>

- gcc flags an issue on leap 15.1 that is a false positive, see
  [gh#lammps/lammps#2078], so disabling lammps custom no optimzation 
  flags, using disable_noopt.patch

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Wed May  6 14:54:14 UTC 2020 - Christoph Junghans <junghans@votca.org>

- bump version to 20200505 (patch)
  - update of the bundled Kokkos library to version 3.1 (Stan
    Moore and the Kokkos developers, SNL) [gh#lammps/lammps#2004],
    [gh#lammps/lammps#2054]
  - new Kokkos styles compute orientorder/atom and coord/atom and
    some related bugfixes/improvements (Stan Moore, SNL)
    [gh#lammps/lammps#1895], [gh#lammps/lammps#1902],
    [gh#lammps/lammps#1906], [gh#lammps/lammps#2033]
  - new fix accelerate/cos and compute viscosity/cos in USER-MISC
    as yet another method to compute viscosity (Zheng Gong, École
    normale supérieure de Lyon) [gh#lammps/lammps#2019]
  - update of the polymorphic pair style with bug fixes and a new
    feature (Xiaoweng Zhou, SNL) [gh#lammps/lammps#2000]
  - added option to create a dummy fix as a placeholder early in
    an input to guarantee placement at the top of the list of
    fixes. (Steve Plimpton, SNL) [gh#lammps/lammps#1760]
  - update to fix bond/react to allow using equal style variables
    a probability input (Wolfgang Verestek, U Stuttgart)
    [gh#lammps/lammps#2013]
  - small update to internal commands in kim_interactions to
    improve KIM simulator model handling (Ronald Miller Carleton
    U, Ryan S. Elliott U Minn), [gh#lammps/lammps#2014]
  - many small fixes and updates to source code (mainly for the
    KOKKOS package), cmake scripts, and documentation to address
    issues with recent changes and minor long-standing issues.
    (multiple authors) [gh#lammps/lammps#2003],
    [gh#lammps/lammps#2006], [gh#lammps/lammps#2010],
    [gh#lammps/lammps#2015], [gh#lammps/lammps#2022],
    [gh#lammps/lammps#2023], [gh#lammps/lammps#2026],
    [gh#lammps/lammps#2027], [gh#lammps/lammps#2030],
    [gh#lammps/lammps#2032], [gh#lammps/lammps#2035],
    [gh#lammps/lammps#2036], [gh#lammps/lammps#2041],
    [gh#lammps/lammps#2043], [gh#lammps/lammps#2044],
    [gh#lammps/lammps#2045], [gh#lammps/lammps#2046],
    [gh#lammps/lammps#2047], [gh#lammps/lammps#2048],
    [gh#lammps/lammps#2049], [gh#lammps/lammps#2051],
    [gh#lammps/lammps#2053], [gh#lammps/lammps#2055]
- enable kokkos and OpenMP

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Wed Mar  4 21:56:52 UTC 2020 - Christoph Junghans <junghans@votca.org>

- bump versoin to 20200303 (stable)
  * General changes
   * The documentation file format has been changed from the custom txt2html markup to using reStructuredText (rst). 
   * Many file read operations are now monitored for read errors and thus allowing to detect damaged or incomplete files like potential parameter files and restart files
   * Updates and improvements to the CMake build system to more closely match all the functionality provided by the conventional make based build system
   * Support for threaded FFTs from FFTW and MKL, support for cuFFT and KISSFFT on the GPU with KOKKOS
   * Expose neighbor lists to the library interface and the Python wrapper
   * Documentation of installing LAMMPS via conda
   * Many small improvements or bugfixes
 * Updates and new commands or styles
   * new dump_modify options to embed ITEM: UNITS and ITEM: TIME with information about units and accumulated simulation time
   * new pair styles cosine/squared, local/density, mesocnt
   * new fix styles wall/reflect/stochastic, propel/self, 'npt/cauchy`
   * new compute gyration/shape/chunk
   * new compute hma for fast, high-precision computation of certain thermodynamic properties of solids
   * new compute style centroid/stress/atom for computing per atom stress in a way allowing for more accurate heat flux computations with interactions involving more than two atoms
   * new third_order command, a companion command to dynamical_matrix, for computing the third order force tensor from finite differences
   * new options ratio and subset for create_atoms and similarly new options type/ratio and type/subset to the set command
   * new tool for post-processing parallel tempering trajectories
   * multiple updates, bugfixes, and improvements to fix bond/react
   * improved implementation of minimization style fire
   * support to run NWChem along with LAMMPS in client/server mode
 * Updates for packages
   * KOKKOS now supports minimization (limited to minimization styles cg and quadratic), updates to the KOKKOS library, general improvements and bugfixes, more styles ported to KOKKOS
   * several new SNAP potentials
   * tweaks to USER-INTEL to compile correctly with too aggressively optimizing compilers, corrections and improvements
   * bugfixes and improvements for the GRANULAR package
   * several new SNAP potentials and a new compute snap for training SNAP potentials
   * bugfixes and improvements to the KIM package, new command kim_param for accessing KIM model parameters
   * updates to the USER-COLVARS package with updates to the included Lepton library
   * updates to the USER-PLUMED package with bugfixes and support for recent releases
   * updates to the USER-CGDNA package including a new coarse grained RNA model (oxRNA2)
   * improvements and updates to the SPIN package, L-BFGS minimizer added
   * updates, extensions, and improvements to the USER-MEAMC package
   * memory leaks fixed when using styles from the GPU with multiple run commands, new pair style lj/cut/tip4p/long/gpu
   * updates to fix rigid variants to add gravity to rigid objects with overlapping (granular) particles
   * support for rerun and read_dump with USER-ADIOS
 * Backward compatibility notices
   * building the USER-COLVARS package with all features enabled now requires a C++-11 compatible compiler
  * due to changes in the random number generator initialization, results when using fix pour, fix deposit, fix evaporate or create_atoms random will not match with previous versions of LAMMPS. see PR #1569
  * the gjf keyword for fix langevin no longer supports the option yes. Instead you have to use either vhalf or vfull
  * the FIRE minimizer has been replaced with an improved implementation. The previous implementation is available as fire/old.
  * new documentation has to be written in reStructuredText format
  
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Fri Nov  1 02:45:27 UTC 2019 - Christoph Junghans <junghans@votca.org>

- generify used mpi version

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Thu Aug 15 21:43:19 UTC 2019 - Christoph Junghans <junghans@votca.org>

- bump versoin to 20190807 (stable)
  * General changes:
    * further tweaks, refactoring, and improvements to building LAMMPS with CMake
    * refactoring of header file handling for improved consistency and removal of cross dependencies
    * refactoring of include keyword processing to lift some limitations and to enable KIM simulator models (see below)
  * Updates for packages:
    * major update of the KIM package to use KIM-API v2.1.x with support for Simulator models and new commands to generate variables for transparent unit conversion in input files
    * optimizations and corrections to the KOKKOS packages, especially when used with CUDA, update of KOKKOS library included in LAMMPS to version 2.9.0
    * updates and bugfixes of the USER-COLVARS package bringing it up to version 2019-08-05
    * new PPPM and Ewald solvers for electric dipoles and nuclear spins
    * optimizations and improvements to pair style and computes in the SNAP package
    * updates, bugfixes and portability improvements for USER-PLUMED package (supports plumed 2.5.2)
    * update to USER-CGDNA package in preparation of supporting an RNA coarse grain force field
    * new keyword hybrid/pair for compute pressure
    * new compute gyration/shape to compute eigenvalues and shape parameters from gyration radius tensor
    * new compute momentum command

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Thu Jun  6 01:58:04 UTC 2019 - Christoph Junghans <junghans@votca.org>

- bump version to 20190605 (stable)
  * General changes:
    + further tweaks and improvements to building LAMMPS with CMake.
    + improved error messages
    + refactoring of Install.py scripts in the lib folders to use the argparse module
   + better checking for style compatibility with suffixed styles
 * New packages:
   + USER-YAFF providing styles for force fields using QuickFF used for simulation of MOFs
   + USER-ADIOS package to provide Exascale compatible I/O support for dump files through the ADIOS v2.x library
 * Updates for packages:
   + consolidation of "soft" pair styles in USER-FEP package and addition of CLASS2 pair style variants.
   + KOKKOS package bugfixes and enhancements (Stan Moore, SNL)
   + new generalized pair style granular (Dan S. Bolintineanu, Ishan Srivastava, Jeremy B. Lechman, SNL)
   + new pair style drip for dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
   + new pair style e3b for adding option to model the E3B water potential (Steven E. Strong, U Chicago)
   + new fix style electron/stopping for modeling energy loss through interactions high speed atoms with electrons
   + update to USER-COLVARS package to version 2019-04-26
   + update of the KIM package to use KIM-API v2.0 (Ryan Elliot, UMN)
   + update to USER-INTEL package to enable use of the package with -DLAMMPS_BIGBIG
   + update to USER-PTM package. examples added, license info updated, documentation updates (Peter Larsen, MIT)
   + updates and additions to the SPIN package (Julien Tranchida, SNL)
   + updates to hyper-dynamics support (Steve Plimpton, SNL)
   + updates, improvements, and bugfixes to fix bond/react (Jake Gissinger, U Colorado)
   + bugfix/refactoring of REBO pair style to correctly implement what is advertised in the documentation.
- enable support for kim through kim-api package

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Tue Dec 11 21:27:58 UTC 2018 - Christoph Junghans <junghans@votca.org>

- bump version to 20181212 (stable)
  * general:
    + major improvements to building LAMMPS with CMake.
    + significant consolidation and improved consistency of the manual after the refactoring for the last stable release
    + reduced risk of memory/buffer overflows by replacing most uses of sprintf() by snprintf()
  * new packages
    + USER-PLUMED package with a native interface (no more patching)
    + USER-SDPD package for smoothed dissipative particle dynamics (SDPD)
    + USER-PTM package for polyhedral template matching analysis to characterize local structure
    + new kspace style scafacos, which interfaces to the ScaFaCoS library of long-range coulomb solvers.
  * updates for packages:
    + USER-COLVARS: updates and bugfixes
    + REPLICA: added support for (local and global) hyperdynamics
    + KOKKOS: updated Kokkos library, added several KOKKOS versions of styles from the GRANULAR package
    + USER-INTEL: updates, bugfixes and improved support for using
    + USER-MISC: new styles, compute pressure/cylinder, fix ffl (fast forward langevin), bugfixes and improvements
    + Many small bugfixes, corrections for memory leaks and memory management inconsistencies and general improvements.
  * Backward compatibility notices:
    + the command line flags -restart and -r are no longer available. 
    + the naming conventions for the group name of groups maintained by fix bond/react have changed. 
    + pair styles in the USER-SPH package no longer support Pair::single().
    + the meaning of the sign of mu in fix atom/swap has been reversed to be consistent with usual conventions.
    + the default installation prefix for CMake based compilation has been changed from /usr/local to $HOME/.local

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Wed Aug 22 18:56:58 UTC 2018 - junghans@votca.org

- bump version to 20180822 (stable)
  * New CMake option for building LAMMPS and all of its packages, as an alternative to traditional make
  * Restructured documentation
  * DEM polygonal and polyhedron particles
  * new compute entropy/atom command
  * New SPIN package for modeling the dynamics of magnetic atomic spins
  * New fix bond/react command to enable simulation of one or more complex heuristic reactions
  * New USER-BOCS package
  * Fixes memory leaks caused when using the GPU package and OpenCL
  * Various other small updates and bugfixes
- drop 858.patch - merged upstream

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Wed Mar 28 16:57:22 UTC 2018 - junghans@votca.org

- bump version to 20180316 (stable)
- many little bugfxes: http://lammps.sandia.gov/bug.html
  * A potentially harmful bug was found and fixed in the pair_style reax/c command
- Added 858.patch to fix return value on ppc64

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Thu Mar  8 20:21:43 UTC 2018 - junghans@votca.org

- bump version to 20180308
- many little bugfxes: http://lammps.sandia.gov/bug.html
  * Various small changes and bug fixes in preparation for a new stable version release

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Mon Mar  5 17:58:23 UTC 2018 - junghans@votca.org

- bump version to 20180222
- many little bugfxes: http://lammps.sandia.gov/bug.html
  * added a pair lj/cut/coul/wolf command to enable Wolf treatment of Coulombic
  * added a new USER-MOFFF package which is an implementation of the MOF-FF (MOF force field)
  * added a new pair_style ufm command

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Sat Jan 27 02:57:30 UTC 2018 - junghans@votca.org

- bump version 20180117
- many little bugfxes: http://lammps.sandia.gov/bug.html
  * new pair yukawa/kk command
  * new fix python/move command for time integration in Python
  * new pair extep command
  * tools/doxygen directory to build a Doxygen style call graph and API lists for LAMMPS
  * new pair snap/kk and pair zbl/kk commands
  * update of Kokkos library
  * improvements to pair reax/c command
  * new info coeffs command option
  * much faster replicate command for large systems when using many processors
  * improved setup performance for large systems on many processors with molecules and pppm
  * more informative error messages when evaluating variables
- dropped 30b482975a6a29db2265b44c4f27d6293eacb72f.patch, got merged

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Fri Jan 19 22:34:55 UTC 2018 - junghans@votca.org

- fix python install for openSUSE Factory

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Sat Nov  4 00:21:36 UTC 2017 - junghans@votca.org

- enable GPU support via OpenCL
- added 30b482975a6a29db2265b44c4f27d6293eacb72f.patch

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Wed Oct 25 23:32:43 UTC 2017 - junghans@votca.org

- bump version 20171023
- many little bugfxes: http://lammps.sandia.gov/bug.html
  * added a new USER-UEF package
  * added a fix rhok command
  * added a bond_style gromos command compatible with the GROMOS force field.
  * added coreshell variants of the pair born/coul/wolf and pair coul/wolf potentials to the CORESHELL package.

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Wed Oct 25 12:45:13 UTC 2017 - junghans@votca.org

- adapt to new openlmi package - source mpivars.h during build

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Mon Sep 11 13:13:20 UTC 2017 - junghans@votca.org

- changes license to GPL-2.0 and GPL-3.0+ (#522368)

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Fri Sep  8 15:44:59 UTC 2017 - junghans@votca.org

- bump version to 20170901
- drop 573.diff, got merge upstream
- many little bugfxes: http://lammps.sandia.gov/bug.html
  * added USER-MESO package
  * new compute aggregate/atom and compute fragment/atom commands

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Tue Aug 15 16:47:20 UTC 2017 - junghans@votca.org

- bump version to 20170811
- many little bugfxes: http://lammps.sandia.gov/bug.html

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Mon Jul 24 23:15:46 UTC 2017 - jengelh@inai.de

- RPM group fix.

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Fri Jul 21 14:47:34 UTC 2017 - junghans@votca.org

- bump version of 20170706 and move to cmake (upstream 573.diff)
- Notable new features in this release are:
  * refactoring of the neighbor list construction to be more modular and extensible from packages. active neighbor list modules
    are reported in the output
  * updates, performance improvements and new styles for the KOKKOS and USER-INTEL packages
  * bugfixes and refactoring of parts of AIREBO and AIREBO-M addressing some of the occasionally observed instabilities with the
    LAMMPS implementation
  * new interface to Multi-Scale Coarse-Graining tools of the Voth group via new MSCG package with fix mscg
  * new pair styles lj/charmmfsw/coul/charmmfsh and lj/charmmfsw/coul/long and dihedral style charmmfsh for improved
    compatibility with the CHARMM code using recent versions of the CHARMM force field
  * several new styles in the USER-MISC package
  * improved compatibility with Python 3 (now only the PYTHON package is still Python 2 only), improvements to PyLammps and its
    documentation
  * various updates and performance improvements for USER-DPD package
  * updates and bugfixes to USER-COLVARS
  * new package USER-CGDNA for coarse grained DNA simulations
  * new support for generalized replica exchange (gREM) via temper/grem and fix grem commands
  * support for treating spherical particles as 2d discs
  * improvements for load balancing via recursive bisectioning
  * new SNAP potential for tungsten and tungsten/helium systems
  * updated version of the bundled moltemplate tool
  * updated tutorial for submitting additions and changes to LAMMPS via GitHub
  * improvements to the documentation build tools
  * ambiguous hyperlinks in documentation are made unique
  * spellchecked documentation and comments
  * removed the obsolete xmovie software
  * many little cleanups, bug fixes and removal of dead or obsolete code, including in the tools folder

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Tue Apr 23 21:30:46 UTC 2013 - scorot@free.fr

- first package

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File lammps.changes of Package lammps (Revision 1737c667ccc13d85323240df796daaa1)

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