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| Name: lammps | Distribution: openSUSE Tumbleweed |
| Version: 20201029 | Vendor: openSUSE |
| Release: 5.4 | Build date: Sat Feb 3 22:18:28 2024 |
| Group: Productivity/Scientific/Chemistry | Build host: obs-power9-12 |
| Size: 430659 | Source RPM: lammps-20201029-5.4.src.rpm |
| Packager: http://bugs.opensuse.org | |
| 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
* Mon May 15 2023 Christoph Junghans <junghans@votca.org>
- Disable kokkos support until the next release will support
kokkos-4
* Wed Dec 07 2022 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- Add Conflicts and Provides to allow upgrade of python package
without conflict.
- Reenable Fortran tests.
- Cleanup spec file.
- Ignore test failures on ix86.
* Wed Dec 07 2022 Steve Kowalik <steven.kowalik@suse.com>
- Do not provide Python 2 package names for Python 3 packages.
- Skip Fortran tests for now.
* Tue Nov 23 2021 Steve Kowalik <steven.kowalik@suse.com>
- Switch to Python 3:
* Rename package to python3-lammps.
* Fri Oct 08 2021 Guillaume GARDET <guillaume.gardet@opensuse.org>
- Disable kokkos on %{arm}
* Fri Oct 01 2021 Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
- Use openmpi macros to always build with the default openmpi version.
* Wed Nov 04 2020 Christoph Junghans <junghans@votca.org>
- dropped 9cdde97863825e4fdce449920d39b25414b2b0b3.patch merged upsteam
- dropped 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch merged upstream
- bump version to 20201029 (stable)
- General changes:
- Significant refactoring of the core LAMMPS code to increase
code reuse, simplify new additions, improve thread safety, and
benefit from C++11 features. In particular the following
changes were incorporated:
- Refactoring of the AtomVec classes to simplify adding new
atom styles to the code. Also adding support for writing
complete data files for atom styles ellipsoid, line, tri,
and body, which had been previously missing.
- Implementation of string tokenizer and potential file reader
classes to improve parsing of text files and avoid the
strtok() function. This has lead to substantial reduction in
the lines of code used for those cases.
- Transferring of utility function from class members to
standalone functions in the utils namespace. Several new
additions of such convenience functions
- Using const std::string & instead char * or const char * as
function argument in many places to simplify string
processing and replacing C style string functions with their
equivalent or expanded functionality of std::string member
functions
- Incorporation of fmtlib to replace and simplify many cases
of output formatting. This avoids many complications with
printf() style functions since no special treatment is
required for processing bigint or tagint arguments. Since
fmtlib has been accepted as a C++20 feature, this is also
future proofing the code base.
- Avoiding use of temporary local buffers for output
formatting and thus lowering the risk of buffer overflows.
This was enabled by the previous two changed.
- Replacing NULL with nullptr where applicable for better
detection of incorrect use.
- Major reorganization and significant expansion of the manual:
- The manual is now split into two parts: a User Guide and a
Programmer Guide
- Most of the content related to using the library interfaces,
the Python module (and Python in general) have been moved to
the Programmer Guide
- The content of the external Developer Guide PDF has been
incorporated into the Programmer Guide section and expanded
- The documentation of the C-library interface and Python
module has been expanded and the documentation of the
individual APIs are now imported from the source code by
means of using doxygen (for C/C++) and docstrings (for
Python).
- Redundancies have been reduced, cross-links added, and links
to external websites checked, updated or removed.
- Addition of a unit test facility which is integrated into
building LAMMPS with CMake and using the ctest tool that comes
with CMake. Tests for a variety of features and styles are
included with a code coverage close to 40%. The added tests
have exposed a significant number of previously unknown bugs
and inconsistencies (e.g. between plain pair styles and
suffixed versions or between Pair::compute() and
Pair::single()) in the code base, which have been fixed.
- Significant refactoring of the LAMMPS C-library interface and
Python module: several new functions were added, especially
for introspection, ad-hoc numerical constants were replaced by
symbolic constants defined in enumerators and synchronized
betwee C and Python, where possible and needed. Most
modifications were
done in a backward compatible way.
- Add support for a "UNITS:" metadata tag to potential and
tabulation files and code to error out if the value does not
match with the current setting. For some potentials, mainly
manybody potentials, support for on-the-fly conversion between
"metal" and "real" units was added, so that a file with
parameters for "metal" units can be used in a simulation with
"real" units, if the pair style supports it.
- Ordering of #include "" statements has been revised and the
lists updated where possible after analyzing with the IWYU
tool.
- Significant refactoring of CMake scripts enabled by moving the
minimum required CMake version from 2.8.x to 3.10.x. CMake
build support is more reliable, portable to different host
operating systems and efficient.
- Conventional build system now always builds the LAMMPS library
and the executable, so the available modes are reduced from 4
to 2: mode=static and mode=shared. The CMake build behaves
equivalently.
- Use pre-processor macros (requiring C++11) to provide
compatibility with OpenMP 4.x and later semantics
- Many small fixes and improvements.
- Removal of outdated or obsolete makefiles. Removal of obsolete
files and folder in the bench folder.
- Updates and new commands or styles or packages:
- New MLIAP package providing a generalized framework for
machine-learning potentials. This currently includes an
implementation of the SNAP potential
- New USER-MESONT package for mesoscale modeling of nanotubes.
- New command reset_mol_ids
- New fix widom for modeling Widom insertions
- New fix pafi to perform langevin or brownian dynamics time
integration constrained to a potential hyperplane. Intended to
be coupled to the PAFI C++ code.
- Bugfixes, improved documentation, and new functionality for
fix bond/react in particular RMSD based constraints.
- New fix accelerate/cos and compute viscosity/cos in USER-MISC
as yet another method to compute viscosity.
- New fix momentum/chunk to remove per chunk momentum
- New bond style special to provide a mechanism to implement
special bond exclusions beyond 1-4.
- Ports of more functionality to the KOKKOS package and several
performance optimizations. Support for AMD GPUs via HIP.
Update of the bundled Kokkos library to version 3.2.
- Support for triclinic cells when using "tiled" communication
style.
- New pair style for charge-dipole damping with Tang-Toennies
function in the USER-DRUDE package
- Updates, bugfixes and adjustments to LAMMPS requiring C++11 in
the USER-COLVARS package (now at version 2020-09-17).
- Support for building triclinic neighbor lists on the GPU in
the GPU package. Bugfixes and performance improvements for GPU
styles.
- Updates to writing binary dump files and binary2atom tool to
become consistent with current text mode custom dumps
- Updates to the user supported examples/COUPLE/fortran and
examples/COUPLE/fortran2 wrappers to become compatible with
updates to the C-library interface. Also work on a new,
"object oriented" Fortran interface has started.
- New LAMMPS shell command as alternative to the regular LAMMPS
executable for improved interactive use.
- Interface file for use with SWIG to create bindings to the
LAMMPS library interface for a wide variety of (mostly
scripted) programming languages (like Java, JavaScript, Lua,
Perl, Ruby, Tcl and more).
- Improved support for cross-compiling binaries for Windows on
Linux. This enables building a liblammps.dll file and loading
the LAMMPS Python module also on Windows.
- Improved CMake support for building with "ninja" instead of
"make".
* Sun Sep 20 2020 Christoph Junghans <junghans@votca.org>
- dropped disable_noopt.patch, merged upstream
- added 9cdde97863825e4fdce449920d39b25414b2b0b3.patch from
https://github.com/lammps/lammps/pull/2381 fix a failing test
- added 61ce73273b3290083c01e6a2fadfb3db0889b9ba.patch from
https://github.com/lammps/lammps/pull/2381 fix another failing test
- bump version to 20200918 (patch)
- New fix pafi to perform langevin or brownian dynamics time
integration constrained to a potential hyperplane. Intended to
be coupled to the PAFI C++ code (Thomas Swinburne, CNRS /CINaM
Marseille and Mihai-Cosmin Marinica, SRMP/CEA Saclay) PR
[gh#lammps/lammps#1472]
- Update of the Kokkos library to version 3.2 (Stand Moore, SNL
and the Kokkos developers), PR [gh#lammps/lammps#2311]
- Updates to KOKKOS package to improve usability with the HIP
backend for AMD GPUs (Nick Curtis) PR [gh#lammps/lammps#2371]
- Update of the USER-COLVARS package to version 2020-09-17
(Giacomo Fiorin, NIH and other Colvars developers) PR
[gh#lammps/lammps#2356], PR [gh#lammps/lammps#2376]
- Change behavior of fix bond/react to update all charges by
default which is the more intuitive behavior. Keywords have
been updated to be more intuitive as well (Jake Gissinger, U
Colorado) PR [gh#lammps/lammps#2368]
- Update of dump styles in the COMPRESS package to be consistent
with recent changes elsewhere, added support for Zstd
compression and the option to set the compression level (Richard
Berger, Temple U), PR [gh#lammps/lammps#2331]
- Use eigensolver contributed to USER-REACTION package to
replace the old "jacobi" function to avoid licensing issues.
Implement wrapper functions around templated implementation
(Andrew Jewett, Scripps), PR [gh#lammps/lammps#2347]
- Small refactor of fix qeq/reax and its USER-OMP and KOKKOS
variants to reduce code replication and allow to add features
(Stan Moore, SNL) PR [gh#lammps/lammps#2354]
- Replace the use of the C-style NULL with the C++11 nullptr
keyword, where meaningful. (E. Anne Gunn, Sheridan College) PR
[gh#lammps/lammps#2358]
- Replace numeric constants in Atom and AtomVec classes by
symbolic ones via enumerators (Axel Kohlmeyer, Temple U) PR
[gh#lammps/lammps#2360]
- Bugfixes for the GPU package and related CMake/make files
(Vsevolod Nikolskiy, HSE University Moscow and Trung Nguyen,
Northwestern U), PR [gh#lammps/lammps#2307], PR
[gh#lammps/lammps#2313], PR [gh#lammps/lammps#2322], PR
[gh#lammps/lammps#2326]
- Bugfix for Langevin thermostatting inside of multiple fix
rigid variants (Trung Nguyen, Northwestern U) PR
[gh#lammps/lammps#2367]
- Refactoring of the C library interface and the Python wrapper
for consistency and maintainability, unit test support for the
interfaces, decoration of library functions with Doxygen comments
for semi-automatic documentation in the manual (Axel Kohlmeyer and
Richard Berger, Temple U) PR [gh#lammps/lammps#2310], PR
[gh#lammps/lammps#2318], PR [gh#lammps/lammps#2320], PR
[gh#lammps/lammps#2357], PR [gh#lammps/lammps#2359], PR
[gh#lammps/lammps#2362]
- Update of documentation build system to include Doxygen
processing and integration of that output via the "breathe"
Sphinx extension inclusion of the Developer Guide in the
manual, update and corrections to the CMake support (Axel
Kohlmeyer and Richard Berger, Temple U) PR
[gh#lammps/lammps#2309], PR [gh#lammps/lammps#2312], PR
[gh#lammps/lammps#2327]
- Update headers in the documentation of LAMMPS style commands
to be more compact and check for missing index entries
(Richard Berger, Temple U) PR [gh#lammps/lammps#2335]
- Update the compilation related documentation to use the
sphinx-tabs extension (in HTML mode only) to make it more
compact (Axel Kohlmeyer, Temple U) PR [gh#lammps/lammps#2348]
- Revised internal and external links in the documentation (Matt
Mansell and others) PR [gh#lammps/lammps#2341]
- Move more convenience functions from classes to the utils
namespace, update the code to consistently use the new
versions and remove the old, update the manual to include the
documentation of those APIs into the developer guide (Axel
Kohlmeyer, Temple U) PR [gh#lammps/lammps#2319], PR
[gh#lammps/lammps#2349]
- Start of a new (and "official") Fortran library interface and
corresponding sphinx API documentation in the programmer guide
plus unit tests for implemented APIs (Axel Kohlmeyer, Temple U) PR
[gh#lammps/lammps#2325]
- Update include file conventions and update lists of include
files accordingly, add make iwyu target to run the
include-what-you-use tool (Axel Kohlmeyer, Temple U) PR
[gh#lammps/lammps#2338]
- Make internal memory usage reporting consistently use the same
data type (Axel Kohlmeyer, Temple U) PR
[gh#lammps/lammps#2363]
- Add support to call reset_mol_ids internally from fix
bond/react (Jake Gissinger, U Colorado), PR
[gh#lammps/lammps#2240]
- Add RMSD based constraint to fix bond/react (Jake Gissinger, U
Collorado, and Andrew Jewett, Scripps, and Yuya Kurebayashi,
Tohoku U) PR [gh#lammps/lammps#2314]
- Refactor of USER-BOCS code to fix memory leaks and memory
access issues (E. Anne Gunn, Sheridan College) PR
[gh#lammps/lammps#2274]
- Implementation of force history for Mindlin variants of the
granular pair style (Jibril B. Coulibaly, Northwestern U), PR
[gh#lammps/lammps#2196]
- Updated singularity container description files to better
support the upcoming stable release (Richard Berger, Temple U)
PR [gh#lammps/lammps#2340]
- Various small updates and corrections (multiple authors) PR
[gh#lammps/lammps#2315], PR [gh#lammps/lammps#2317], PR
[gh#lammps/lammps#2336], PR [gh#lammps/lammps#2344], PR
[gh#lammps/lammps#2353], PR [gh#lammps/lammps#2364], PR
[gh#lammps/lammps#2366], PR [gh#lammps/lammps#2373], PR
[gh#lammps/lammps#2369], PR [gh#lammps/lammps#2375]
* Sun Jun 14 2020 Christoph Junghans <junghans@votca.org>
- disable march=native optimization by setting empty
CMAKE_TUNE_FLAGS
* 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].
/usr/bin/binary2txt /usr/bin/chain.x /usr/bin/lammps-shell /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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