Changelog for liblammps0-20201029-65.80.i586.rpm :

* Mon May 15 2023 Christoph Junghans - Disable kokkos support until the next release will support kokkos-4
* Wed Dec 07 2022 Stefan Brüns - 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 - Do not provide Python 2 package names for Python 3 packages.- Skip Fortran tests for now.
* Tue Nov 23 2021 Steve Kowalik - Switch to Python 3:
* Rename package to python3-lammps.
* Fri Oct 08 2021 Guillaume GARDET - Disable kokkos on %{arm}
* Fri Oct 01 2021 Nicolas Morey-Chaisemartin - Use openmpi macros to always build with the default openmpi version.
* Wed Nov 04 2020 Christoph Junghans - 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 - 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 - disable march=native optimization by setting empty CMAKE_TUNE_FLAGS
* Wed May 13 2020 Christoph Junghans - 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].