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| Name: lammps | Distribution: openSUSE:Factory:zSystems |
| Version: 20200505 | Vendor: obs://build.opensuse.org/openSUSE:Factory:zSystems |
| Release: 1.1 | Build date: Fri Jun 12 13:23:59 2020 |
| Group: Productivity/Scientific/Chemistry | Build host: s390zp21 |
| Size: 155111 | Source RPM: lammps-20200505-1.1.src.rpm |
| Url: https://lammps.sandia.gov | |
| Summary: Molecular Dynamics Simulator | |
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
GPL-2.0-only AND GPL-3.0-or-later
* Wed May 13 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].
* Sun May 10 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
* Wed May 06 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
* Wed Mar 04 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
* Fri Nov 01 2019 Christoph Junghans <junghans@votca.org>
- generify used mpi version
* Thu Aug 15 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
* Thu Jun 06 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
* Tue Dec 11 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
* Wed Aug 22 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
* Wed Mar 28 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
* Thu Mar 08 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
* Mon Mar 05 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
* Sat Jan 27 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
* Fri Jan 19 2018 junghans@votca.org
- fix python install for openSUSE Factory
/usr/bin/binary2txt /usr/bin/chain.x /usr/bin/lmp /usr/bin/msi2lmp /usr/share/doc/packages/lammps /usr/share/doc/packages/lammps/README /usr/share/licenses/lammps /usr/share/licenses/lammps/LICENSE /usr/share/man/man1/lmp.1.gz /usr/share/man/man1/msi2lmp.1.gz
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