lammps

Changes since the 23 June 2022 patch release:

• New AMOEBA package with an implementation of the AMOEBA and HIPPO polarizable force fields from the Tinker MD code (Josh Rackers and Steve Plimpton, SNL and Trung Nguyen U Chicago) PR #2898
• New compute styles sna/grid and sna/grid/local for the ML-SNAP package (Aidan Thompson, SNL and Lenz Fiedler, HZDR) PR #3305
• New pair style srp/react in the MISC package (Vaibhav Palkar, Clemson) PR #3337
• Enhancements to the MDI Package with expanded functionality (Steve Plimpton, SNL and Taylor Barnes, MolSSI) PR #3307, PR #3336
• Rename CG-SDK package to CG-SPICA and rename all related commands, new functional form LJ12-5 (in addition to LJ12-6 and LJ12-4, and LJ9-6) (Yusuke Miyazaki, Okayama U) PR #3343
• Add KOKKOS package version of the MEAM package (Naga Vydyanathan, NVIDIA and Stan Moore, SNL) PR #3328
• Update bundled Kokkos library to version 3.6.1 (Stan Moore, SNL and the Kokkos developers) PR #3329
• New "threebody on/off" keyword for pair style sw that allows turning off the three-body term calculation and enabling performance optimizations for that case (Jackson Elowitt, U Utah) PR #3316
• Optimizations for reading large blocks of input (Steve Plimpton, SNL) PR #3323
• Corrections and enhancements to how groups are processed in compute contact/atom (Joel Clemmer, SNL) PR #3339
• Add "pair_modify neigh/trim yes/no" option to allow to build optimized, trimmed neighbor lists for hybrid/overlay (Stan Moore, SNL) PR #3341
• Add "timestep yes/no" option to the read_dump command to simplify simulation loops where atoms are added from a dump file (Axel Kohlmeyer, Temple U) PR #3344
• Improved detection of Python interpreter and libraries in CMake to be more consistent across platforms, CMake versions and better honor the documented ways to override the automatic choice (Axel Kohlmeyer, Temple U) PR #3355
• Update of bundled linalg library to LAPACK version 3.10.1 plus adding ZHEEVD and dependencies and a new CMake setting -DUSE_INTERNAL_LINALG to allow preferring the bundled library over external ones (Axel Kohlmeyer, Temple U) PR #3360
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3317, PR #3319, PR #3322, PR #3327, PR #3298, PR #3330, PR #3331, PR #3340 , PR #3342, PR #3346, PR #3349, PR #3350, PR #3358, PR #3359, PR #3361, PR #3364, PR #3365, PR #3370, PR #3372, PR #3374, PR #3377

Backward compatibility notes:

• the command fix mdi/aimd has been renamed to fix mdi/qm
• the new pair_modify neigh/trim option defaults to yes. Use it with no in case simulations with hybrid/overlay fail and report the details in a new issue here
• the CG-SDK package has been renamed CG-SPICA, all style have been renamed accordingly, but backward compatibility to the old names is included

Below is a list of major changes since the last stable release 29 September 2021

This stable release adds about 3000 commits since the previous stable release. This includes many contributions from beyond the core LAMMPS developers, but also continues the internal refactoring of the code base to make it more consistent and reliable yet also take more advantage of C++ features where they help to simplify the code and easier to modify, maintain, and contribute to.

With this release we will remove the previously used branches master and unstable and use the current equivalents develop and release. The stable keeps its name, but since we published bugfix updates to the last stable release it will now run parallel to develop and be explicitly synchronized with it (technically speaking, the patch_23Jun2022 and the stable_23Jun2022 tags will point to different commit hashes due to the difference in their histories, but the content will be identical).

General Changes

• Continued refactoring of the core LAMMPS code and many packages to increase code reuse, simplify new additions, improve consistency, and benefit from C++11 features. Several convenience functions and classes were added in the process.
• New platform namespace with abstractions for platform specific operations or getting information about platforms and tools. This includes dynamic loading of shared objects and file and directory operations.
• start ongoing project to change how errors and warnings are reported and documented
• Improved portability, especially to Windows. It is now possible to build most of LAMMPS (including unit testing) natively on Windows with Visual Studio 2022 and MSVC++ compilers or Clang or Intel OneAPI compilers. Settings for Visual Studio are included.
• Improved plugin mechanism and option to automatically load custom plugins that are either not distributed with LAMMPS or depend on libraries that have licensing terms or technical requirements preventing linking them into LAMMPS directly. Examples for how to build such plugins for the KIM and the ML-PACE package are included. For the latter also a NSIS script to build an installer for Windows.
• Semi-automatic refactoring with clang-tidy: this has updated the coding style to take advantage of C++11 features and make things more explicit, so the compiler can warn more easily about problems. Also, clang-format is now applied to more files.
• update force style unit tests to work with Kokkos + OpenMP
• Refactor handling of thermodynamic output for better readability and add new thermo_style "yaml"
• Automatically load plugins in folders listed in the LAMMPS_PLUGIN_PATH environment variable
• More content and improvements for the Programmer Guide section of the Manual

Updates and new commands or styles or packages:

• New fix acks2/reaxff for ACKS2 charge equilibration and updates to fix qeq/reaxff that add support for fix efield to both charge equilibration methods.
• New fix mol/swap for swapping of atom types within a single, randomly selected molecule
• Add support for multi-species potentials to ML-PACE package
• Allow GPU package pair styles to be used with newton_pair on
• New pair style sw/mod providing an empirically modified Stillinger-Weber potential suitable for compounds like MoS2
• New pair style nm/cut/split and bond style fene/nm for coarse grain polymer models
• Support for binary native dump files for read_dump and rerun
• Updated singularity/apptainer definition files
• New compute ave/sphere/atom to compute averaged properties in a sphere around atoms
• Support writing to dump files at regular time interface for variable timestep simulations
• Add centroid atomic stress support for shake, rattle and rigid/small fixes
• Add new pair style harmonic/cut providing a repulsive-only harmonic potential
• Add new fix numdiff/virial for deriving virial stress from potential energy via numerical differences
• Add two new interlayer pair styles ilp/tmd and saip/metal
• new option for multi-file dumps to have files that are more evenly sized to address post-processing and visualization issues for simulations of very large systems
• accelerator support (including KOKKOS) and improvements for dynamical_matrix and third_order commands
• re-implementation of the tools/eam_database Fortran code in Python
• update setup.py and install.py for python module to use setuptools instead of deprecated distutils and build a binary wheel file
• Add computes for local components of the pressure tensor in cartesian and spherical coordinates
• Major update of the LATBOLTZ package
• Code optimization for several KOKKOS styles
• Add fixes for damping of rotational and translational energy for extended particles
• Add support for an inner cutoff switching function to SNAP related commands that smoothly turns of SNAP descriptors at short range
• Memory usage optimization and bugfix for mesocnt pair style
• new BPM package for bonded particle models
• new ELECTRODE package
• updates and additions to the DIELECTRIC package
• new compute fep/ta for the FEP package implementing test-area perturbation
• new pair styles ilp/graphene/hbn/opt, ilp/tmd/opt, and saip/metal/opt for the OPT package with 2x speedup
• new pair styles smatb and smatb/single for the SMTBQ package
• new dump_style yaml command in the EXTRA-DUMP package
• add Kspace support to the PLUGIN package
• enhancements and additions for the MDI package. This obsoletes the MESSAGE package.
• additions to the BROWNIAN package to support different rotational and translational temperatures and option to constrain rotation in a plane in 3d
• additions to PyTorch support in ML-IAP packge
• new compute born/matrix command to compute elastic stress
• add KOKKOS package versions of the pair styles from the DPD-BASIC package
• add KOKKOS package version of pair style adp
• new colname option for dump_modify and thermo_modify to replace the column header strings for thermo output or in dump files
• add support for writing yaml format files to fix ave/time and also support fix_modify colname similar to thermo and dump
• add support for angle styles to fix adapt and add or update "extract()" methods to some angle/bond styles and make the extract arguments more consistent
• add region style ellipsoid
• add "aveabs" and "sumabs" options to compute reduce
• add "variable" option to delete_atoms command
• bugfix for DOF handling in compute temp/profile
• more consistent behavior of dynamic groups through moving the invocation of the internal fix to a later time in the timestep
• make time thermo property restartable and implement a reset_timestep time option to set it manually
• remove support for legacy GPU hardware and CUDA toolkits in the GPU package
• Update of the bundled Kokkos library to version 3.6.0
• Update of the bundled Colvars library to version 2022-05-24
• Add KOKKOS package version of the pace pair style from the ML-PACE package
• New pair styles "sw/angle/table" and "threebody/table" for the MANYBODY package
• Add support for GPU accelerated FFTs with HIP and KOKKOS
• Add support for SO3 descriptors to the ML-IAP package
• New "overlap" option for create_atoms random that will avoid close contacts
• New "mesh" option for create_atoms to approximate meshes from STL files with atoms
• Add timer style variables for measuring wall time in seconds from the input script

Backward compatibility notices:

• delete_atoms porosity has been renamed to delete_atoms random and uses/supports different options
• The CC.Lebedeva interlayer potential file has been updated. It now uses by default parameters for "normal" conditions. The previous default parameters are tuned for high-pressure conditions and are still available when using "C1" instead of "C" as element.
• Using the PyLammps python module now requires the presence of numpy
• The new version of make install-python will not install a package over an existing package as the old version did. Instead, it will attempt to uninstall the old package and then install the new version. Packages installed with distutils, like the old version of make install-python, must be manually uninstalled (they don't store a suitable manifest). This should only be needed once, since from then on uninstall should be possible.
• The update to the LATBOLTZ package is a significant update that changes the syntax of the fix lb/fluid command in a way that is not backward compatible. Inputs must be updated accordingly. Also fixes lb/pc and lb/pc/rigid/sphere have been removed and fixes nve and rigid should be used in their stead.
• The thermodynamic output format is slightly changed. This may break parser implementations for analysis of LAMMPS log files that are not indifferent to whitespace changes and width of fields.
• the MESSAGE package has been removed. its functionality is provided in a more general way by the MDI package
• the GPU package using CUDA now requires CUDA toolkit version 8 or later and GPU architector 3.0 (aka Kepler or later). When compiling for OpenCL, driver support for OpenCL 1.2 is required. OpenCL can provide support for GPUs not supported by the CUDA toolkit anymore.
• the bug fix to the DOF calculation in compute temp/profile changes the results (usually by a small margin)

This patch contains the final changes to update the 2 June 2022 release to the 23 June 2022 stable release.

There are no substantial new features in this patch, only a variety of small updates and bug fixes for reported issues and based on extended testing. Notable changes are:

• Refactoring of the plugin examples and a new example building the ML-PACE package as plugin including creating a windows installer. (Axel Kohlmeyer, Temple U) PR #3290
• Bugfix for atom style dielectric
• Bugfix for dump style xtc on Windows (Issue #3292)
• Bugfix for dump style yaml when running in parallel PR #3309
• Change "remap semantics" for the read_restart command to always use the remap option by default and offer an "noremap" option to be able to change to the old behavior. (Issue #3078)
• Bugfix for accessing local computes in Python via NumPy, support LMP_SIZE_VECTOR as alias for LMP_SIZE_ROWS with local computes PR #3309
• Updates and bugfixes for the "Fortran2" and "Fortran_dftb" Fortran interfaces, PR #3312
• Improvements to compute ave/sphere/atom (Stan Moore, SNL) PR #3293
• Fix integer overflow bug in Kokkos version of ReaxFF (Stan Moore, SNL) PR #3295
• Updates to singularity/apptainer container definition files PR #3290
• GitHub actions updates PR #3299, PR #3301, PR #3303, PR #3304
• Recover building binary python wheel file after upgrade to use venv instead of virtualenv. When running with an active virtual environment, the wheel will be installed into the virtual environment as to be expected instead of the system or user site-packages folder PR #3306
• Various small improvements and small corrections to build system, compiler settings, and documentation. PR #3296, PR #3300

This is the first release candidate for the next stable release of LAMMPS. Please test thoroughly and report bugs immediately.

Changes since the 4 May 2022 patch release:

• Update of the bundled Kokkos library to version 3.6.0 (Stan Moore, SNL and the Kokkos developers) PR #3251
• Update of the bundled Colvars library to version 2022-05-24 (Giacomo Fiorin, NIH and the Colvars deverlopers) PR #3260, PR #3286
• Add KOKKOS package version of the pace pair style from the ML-PACE package (Stan Moore, SNL) PR #3264, PR #3278
• New pair styles "sw/angle/table" and "threebody/table" for the MANYBODY package (Christoph Scherer, Max Planck Institute for Polymer Research Mainz) PR #3279
• Add support for GPU accelerated FFTs with HIP and KOKKOS (Emily Kahl, The University of Queensland) PR #3237
• Add support for SO3 descriptors to the ML-IAP package (Aloïs Castellano, University of Liège) PR #3263
• New "overlap" option for create_atoms random that will avoid close contacts (Eugen Rožić, Institute Ruđer Bošković, and Steve Plimpton, SNL) PR #3119
• New "mesh" option for create_atoms to approximate meshes from STL files with atoms (Axel Kohlmeyer, Temple U and Joel Clemmer, SNL) PR #3258
• Add timer style variables for measuring wall time in seconds from the input script (Steve Plimpton, SNL) PR #3255
• Optimizations for compute orientorder/atom (Tomas Oppelstrup, LLNL and Stan Moore, SNL) PR #2988
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3250, PR #3259, PR #3262, PR #3267, PR #3268, PR #3269, PR #3271, PR #3272, PR #3275, PR #3276, PR #3277, PR #3280, PR #3281, PR #3284, PR #3285, PR #3288, PR #3289

Backward compatibility notices:

• The delete_atoms porosity option has been renamed to random and generalized to support multiple sub-styles that have adjustable behavior with respect to exactness and performance of the deletion.

Changes since the 24 March 2022 patch release:

• new BPM package for bonded particle models (Joel Clemmer, SNL) PR #2906
• new ELECTRODE package (Ludwig Ahrens-Iwers and Robert Meißner, Hamburg University of Technology and Shern Tee, University of Queensland) PR #3194
• updates and additions to the DIELECTRIC package (Trung Nguyen, U Chicago) PR #3212
• new compute fep/ta for the FEP package implementing test-area perturbation (Shifeng Ke, Zhejiang University) PR #3192
• new pair styles ilp/graphene/hbn/opt, ilp/tmd/opt, and saip/metal/opt for the OPT package with 2x speedup (Ping Gao and Xiaohui Duan, National Supercomputing Center in Wuxi) PR #3228, PR #3242
• new pair styles smatb and smatb/single for the SMTBQ package (Daniele Rapetti - Politecnico di Torino) PR #3031
• new dump_style yaml command in the EXTRA-DUMP package (Axel Kohlmeyer, Temple U) PR #3205
• add Kspace support to the PLUGIN package (Jinzhe Zeng, Rutgers University) PR #3188
• enhancements and additions for the MDI package. This obsoletes the MESSAGE package. (Steve Plimpton, SNL and Taylor Barnes, MolSSI) PR #2921, PR #3207, PR #3218
• additions to the BROWNIAN package to support different rotational and translational temperatures and option to constrain rotation in a plane in 3d (Sam Cameron, University of Bristol) PR #3193
• additions to PyTorch support in ML-IAP packge (Charlie Sievers) PR #3182
• new compute born/matrix command to compute elastic stress (Germain Clavier - TU Eindhoven) PR #3093
• add KOKKOS package versions of the pair styles from the DPD-BASIC package (Matt Bettencourt, Nvidia) PR #3198
• add KOKKOS package version of pair style adp (Vladislav Galigerov and Vsevolod Nikolskiy, Higher School of Economics, Russia) PR #3247
• KOKKOS optimizations and bugfixes: GPU optimizations for neighbor lists and ReaxFF (Stan Moore, SNL and Evan Weinberg, NVIDIA) PR #3187, PR #3195, PR #3203
• new colname option for dump_modify and thermo_modify to replace the column header strings for thermo output or in dump files (Axel Kohlmeyer, Temple U) PR #3197
• add support for writing yaml format files to fix ave/time and also support fix_modify colname similar to thermo and dump (Axel Kohlmeyer, Temple U) PR #3240
• add support for angle styles to fix adapt and add or update "extract()" methods to some angle/bond styles and make the extract arguments more consistent (Steve Plimpton, SNL) PR #3229, PR #3236
• add region style ellipsoid (Evangelos Voyiatzis, NovaMechanics Ltd) PR #2871
• add "aveabs" and "sumabs" options to compute reduce (Tim Bernhard, ETH Zürich) PR #3246
• add "variable" option to delete_atoms command (Axel Kohlmeyer, Temple U) PR #3243
• bugfix for DOF handling in compute temp/profile (Stephen Sanderson, University of Queensland) PR #2667
• more consistent behavior of dynamic groups through moving the invocation of the internal fix to a later time in the timestep (Steve Plimpton, SNL with an assist from Davie Quigley, U Warwick) #3224
• make time thermo property restartable and implement a reset_timestep time option to set it manually (Axel Kohlmeyer, Temple U) PR #3248
• remove support for legacy GPU hardware and CUDA toolkits in the GPU package (Axel Kohlmeyer, Temple U) PR #3213
• start project to change how errors and warnings are reported and documented (Axel Kohlmeyer, Temple U and Steve Plimpton, SNL) PR #3226, PR #3227, PR #3231
  • Error and warning message docs from header files are removed
  • A new document is started collecting and discussing/explaining errors that are frequently discussed or looked up. Each paragraph is assigned an error code, corresponding error messages have a string added with an URL to the online documentation pointing to those newly added paragraphs
  • Individual "short" error messages like "Illegal xxxx command" are expanded to provide more details to make them (mostly) self-explanatory and thus reduce the need to look them up in the source code
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3186, PR #3189, PR #3191, PR #3196, PR #3199, PR #3201, PR #3202, PR #3206, PR #3208, PR #3210, PR #3211, PR #3214, PR #3215, PR #3216, PR #3217, PR #3219, PR #3220, PR #3221, PR #3222, PR #3223, PR #3225, PR #3230, PR #3232, PR #3233, PR #3234, PR #3238, PR #3241

Backward compatibility notes:

• the MESSAGE package has been removed. its functionality is provided in a more general way by the MDI package
• the GPU package using CUDA now requires CUDA toolkit version 8 or later and GPU architector 3.0 (aka Kepler or later). When compiling for OpenCL driver support for OpenCL 1.2 is required, which usually supports GPUs not supported by the CUDA toolkit anymore.
• the bug fix to the DOF calculation in compute temp/profile changes the results (usually by a small margin)

Changes since the 17 February 2022 patch release:

• Add computes for local components of the pressure tensor in cartesian and spherical coordinates (Olav Galteland, Norwegian U of Science and Technology) PR #3165
• Major update of the LATBOLTZ package (Colin Denniston and collaborators, UWO) PR #3167
• Code optimization for several KOKKOS styles (Nicholas Curtis and Leopold Grinberd and Gina Sitaraman, AMD, Stan Moore, SNL) PR #3147, PR #3158, PR #3169
• Add fixes for damping of rotational and translational energy for extended particles (Jibril B. Coulibaly. Northwestern U) PR #3181
• Add support for an inner cutoff switching function to SNAP related commands that smoothly turns of SNAP descriptors at short range (Aidan Thompson, SNL) PR #3173
• Refactor code for neighbor list requests so that no direct access to the list of requests is needed and settings are as automatic and consistent as possible (Axel Kohlmeyer, Temple U) PR #3159
• Refactor handling of thermodynamic output for better readability and add new thermo_style "yaml" (Axel Kohlmeyer, Temple U) PR #3179
• Replace usage of non-reentrant strtok() and improve file reading and parsing using file reader and tokenizer classes (Axel Kohlmeyer, Temple U) PR #3180
• Memory usage optimization and bugfix for mesocnt pair style (Philipp Kloza, Cambridge U) PR #3162
• Refactor python/install.py script and change installation of the LAMMPS python module via make install-python from using distutils to setuptools. This is now a 2-step process of first creating a binary wheel (.whl) package and then installing it via pip.
• Automatically load plugins in folders listed in the LAMMPS_PLUGIN_PATH environment variable (Axel Kohlmeyer, Temple U) PR #3170
• Add tests for various compute (Axel Kohlmeyer, Temple U) PR #3163
• More content and improvements for the Programmer Guide section of the Manual (multiple authors) PR #3146
• update sphinx theme for the HTML version of the manual (Axel Kohlmeyer, Temple U) PR #3178
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #3138, PR #3139, PR #3141, PR #3142, PR #3145, PR #3148, PR #3153, PR #3155, PR #3156, PR #3161, PR #3164, PR #3166, PR #3168, PR #3171, PR #3174, PR #3177, PR #3185

Backward compatibility notices:

• The new version of make install-python will not install a package over an existing package as the old version did. Instead, it will attempt to uninstall the old package and then install the new version. Packages installed with distutils, like the old version of make install-python, must be manually uninstalled (they don't store a suitable manifest). This should only be needed once, since from then on uninstall should be possible.
• The update to the LATBOLTZ package is a significant update that changes the syntax of the fix lb/fluid command in a way that is not backward compatible. Inputs must be updated accordingly. Also fixes lb/pc and lb/pc/rigid/sphere have been removed and fixes nve and rigid should be used in their stead.
• The thermodynamic output is slightly changed. This may break parser implementations for analysis of LAMMPS log files that are not indifferent to whitespace changes and width of fields. Please note the addition of thermo style "yaml" that should provide a mechanism that should make the process of extracting thermodynamic output data more reliable and easier to realize.

This is the third and final update to the 29 September stable release that fixes bugs that have been reported since the second update and backported from the develop branch.

The following individual changes are included:

• remove obsolete check so that larger systems can be run with ReaxFF
• update the Fortran source code in tools/eam_database to produce files with fewer oscillations and better precision. add python version.
• fix problems causing crashes with the MSM kspace style when continuing a run without and with changing box settings
• avoid using an outdated list of special neighbors when applying the angle constraint in fix bond/create/angle
• fix bug in fix rigid/npt/small and fix rigid/nvt/small leading to NaNs for 2d systems
• fix memory leaks and avoid accessing uninitialized data
• fix a tag caching and skip list generation issue causing crashes when using pair style sw/intel with hybrid pair styles
• fix off-by-one bug in dihedral style fourier/intel
• fix neighborlist and buffer creation bug in pair style lj/long/coul/long/intel
• fix uninitialized data bug in pair style lj/cubic when mixed coefficients where specified explicitly
• fix bug in write_coeff that could not correctly operate on full pathnames
• fix a problem loading the shared library under MacOS after installing the LAMMPS python module with "make install-python"
• adjust package list to avoid compilation failures when using the "most" preset
• improve cythonize detection on machines using bourne shells different from bash (e.g. debian/ubuntu)
• correct handling of make package-update for ML-IAP package
• python 3 compatibility updates scripts in tools/python
• try harder to find the stub version of libcuda.so as provided by the CUDA toolkit in case there is no CUDA driver installation
• fixes to CMake build for ML-QUIP package when using CMake 3.16 and newer or recent Cray Programming Environment versions

Changes since the 7 January 2022 patch release:

• Add new pair style harmonic/cut providing a repulsive-only harmonic potential (Axel Kohlmeyer, Temple U) PR #3087
• Add new fix numdiff/virial for deriving virial stress from potential energy via numerical differences (Aidan Thompson, SNL and Charlie Sievers, UC Davies) PR #3105
• Add two new interlayer pair styles ilp/tmd and saip/metal (Wengen Ouyang, Wuhan University) PR #3125
• Refactor source code to replace use of the virtual keyword in derived classes with the equivalent override which allows to detect some common problems at compile time (Richard Berger, Temple U) PR #3090
• new option for multi-file dumps to have files that are more evenly sized to address post-processing and visualization issues for simulations of very large systems (Stan More, SNL) PR #3097, PR #3110
• accelerator support (including KOKKOS) and improvements for dynamical_matrix and third_order commands (Charlie Sievers, UC Davis) PR #2233
• performance improvements and added unit tests for oxdna atom style (Oliver Henrich, Strathclyde U) PR #3104
• Portability updates for PyLammps (Richard Berger, Temple U) PR #3115
• re-implementation of the tools/eam_database Fortran code in Python (Germain Clavier, TU Eindhoven) PR #3126
• port bundled unit tests and external OpenCL ICD loader to be compiled and run on Windows using the MSVC toolchain (Axel Kohlmeyer, Temple U) PR #3102, PR #3116, PR #3127
• update force style unit tests to work with Kokkos + OpenMP (Richard Berger, Temple U) PR #3035
• update setup.py in python module to use setuptools instead of deprecated distutils (Richard Berger, Temple U) PR #3101
• various optimizations, corrections, refactoring, and compatibility updates for the KOKKOS package (Stan Moore, SNL and multiple collaborators) PR #3082, PR #3088, PR #3092, PR #3100, PR #3111
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #3089, PR #3091, PR #3095, PR #3103, PR #3117, PR #3120, PR #3123, PR #3124, PR #3129, PR #3130, PR #3133, PR #3134, PR #3136

Backward compatibility notices:

• Using the PyLammps python module now requires the presence of numpy

Changes since the 14 December 2021 patch release:

• New compute ave/sphere/atom to compute averaged properties in a sphere around atoms (Stan Moore with Mitch Wood, SNL) PR #2996
• Support writing to dump files at regular time interface for variable timestep simulations (Michal Kanski, Jagiellonian U, and Steve Plimpton, SNL) PR #3052
• Add centroid atomic stress support for shake, rattle and rigid/small fixes (Donatas Surblys, Tohoku U) PR #3046
• Update fmtlib to version 8.1.1 (Axel Kohlmeyer and Richard Berger, Temple U) PR #3073
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #3021, PR #3060, PR #3062, PR #3064, PR #3065, PR #3068, PR #3069, PR #3071, PR #3072

Backward compatibility notices:

• Forces and energies from class2 angle styles may differ due to a bugfix. Previously distances from the BondBond terms were used for BondAngle terms. Commonly those distance settings would be the same and in those cases the results will match.

This is the second update to the 29 September stable release that fixes bugs that have been reported since the first update and backported from the develop branch.

The following individual changes are included:

• fix bug in compute temp/rotate due to uninitialized data cause by a class member shadowing a base class member
• plug minor memory leaks in MACHDYN package
• plug memory and file descriptor leak when reading ReaxFF potential files
• fix internal fix and compute ID clash when using fix reaxff/species multiple times
• fix segmentation fault when using atom style smd as part of a hybrid pair style
• fix communication bug in pair style local/density
• fix segmentation fault due to an uninitialized array in fix nve/gpu when the group is not "all" but there is only one atom type
• fix bugs in eam/cd pair style reported in issue #3074
• correct documentation and potential parameters for Lebedeva interlayer potential
• update names and description of git branches in the manual to reflect the current status and policies
• avoid issues when testing dump commands in parallel
• avoid issues from oversubscribing processors with parallel tests using MPI
• correct error in the documentation for pair style granular
• fix bug in cmake parsing of the version.h file for stable branch. Fixes #3038
• fix bug in bond/angle style table reported in PR #3076 (but fixed differently)

Changes since the 27 October 2021 patch release:

• Update bundled copy of the Kokkos library to version 3.5.0 (Stan Moore, SNL and the Kokkos developers) PR #3019, PR #3053
• Allow GPU package pair styles to be used with newton_pair on (Trung Nguyen, Northwestern) PR #2867
• New update to delete_atoms porosity so that atoms can now be selected by region and group (Steve Plimpton, SNL) PR #2984
• New pair style sw/mod providing an empirically modified Stillinger-Weber potential suitable for compounds like MoS2 (Jin-Wu Jiang, Shanghai University, Wengen Ouyang, Wuhan University) PR #3041
• New pair style nm/cut/split and bond style fene/nm for coarse grain polymer models (Joseph Dietz, Robert Hoy, USF) PR #2958
• Support for binary native dump files for read_dump and rerun (Lixin Sun, Harvard) PR #3054, PR #3059
• Update included fmtlib sources to version 8.0.1 (Richard Berger and Axel Kohlmeyer, Temple U) PR #2809
• Refactoring of access to lists of computes, fixes and regions that do not require access to internal data structures (Axel Kohlmeyer, Temple U) PR #3001
• Refactoring of data file section reading and writing for fixes for more consistency and simpler, more intuitive input (Axel Kohlmeyer, Temple U) PR #3012
• Updated singularity container definition files for building LAMMPS (Richard Berger, Temple U) PR #3043
• Added labels "slow" and "unstable" to some unit tests run with ctest so they can be easily excluded (Richard Berger, Temple U) PR #3033
• Improved support for multi-configuration builds (required on Windows) and passing settings to external projects (Axel Kohlmeyer, Temple U) PR #2940
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #3011, PR #3013, PR #3014, PR #3015 , PR #3017, PR #3020, PR #3027, PR #3032, PR #3034, PR #3040, PR #3044, PR #3049, PR #3055, PR #3056, PR #3058

Backward compatibility notices:

• delete_atoms porosity requires a group as an additional argument
• The CC.Lebedeva interlayer potential file has been updated. It now uses by default parameters for "normal" conditions. The previous default parameters are tuned for high-pressure conditions and available when using "C1" instead of "C" as element.

This is an update to the 29 September stable release that fixes some bugs that have been reported since then and addresses some issues related to compatibility with GitHub, Python and Python package versions used to build the manual, and running the automated unit tests.

The following individual changes are included:

• Corrections to double precision support detection for the GPU package. Only report compatible GPUs. Also consider single-precision FFT requirement for pppm when running unit tests.
• Fix bugs leading to deadlocks when loading INTERLAYER package potential files in parallel
• Correct thermo output when expanding per-atom properties
• Fix compilation issue for QM/MM front end code
• Fix bugs in dump style custom when using custom per-atom data for thresholds
• Update VTK package to compile and work with custom per-atom arrays
• plug some minor memory leaks
• fix some bugs in the KOKKOS package
• update required python package versions for building the documentation to be compatible with python 3.10
• fix memory allocation bug in angle and bond style gaussian leading to memory corruption on 32-bit machines
• fix false positives in python unit tests when LAMMPS is compiled with an external KOKKOS library
• update the citation info for the new LAMMPS paper
• change references to git:// protocol to use https:// protocol instead due to heightened security requirements at GitHub
• document size limitations when sorting dumps
• avoid false positives in unit testing due to numerics and oversubscribing of MPI processes

Important note about branch names

The LAMMPS project has changed the names of its main branches in the git repository to better represent the state of the code. The master branch was renamed to develop and the unstable branch became release. If you are following the git repository to obtain the LAMMPS source code, please update your checkouts and forks accordingly. For a limited time the master and unstable branches will be kept in sync with develop and release (through fast forwarding), but those branches will be removed eventually and then you will be required to use the new branch names or not have access to updates anymore.

Changes since the 29 September 2021 patch release:

• New fix acks2/reaxff for ACKS2 charge equilibration and updates to fix qeq/reaxff that add support for fix efield to both charge equilibration methods. (Metin Aktulga, MSU and Stan Moore, SNL) PR #2931
• New fix mol/swap for swapping of atom types within a single, randomly selected molecule (Steve Plimpton, SNL) PR #2992
• Add support for multi-species potentials to ML-PACE package (Yury Lysogorskiy and the PACE library developers) PR #2968
• Preliminary support for OpenMPTarget in KOKKOS package (Rahul Gayatri, NERSC, Chris Knight, ANL, Stan Moore, SNL) PR #2997
• Implemented and applied a new namespace platform with abstractions of functionality that has either different behavior or uses different APIs on different platforms and operating systems. This reduces code redundancy and enhances platform neutrality of the core LAMMPS code. (Axel Kohlmeyer, Temple U) PR #2979
• Implemented and applied a utility function to parse boolean arguments to keywords (yes/no, on/off, true/false) (Axel Kohlmeyer, Temple U), PR #2951
• Semi-automatic code refactoring using clang-tidy. See issue #2946 for a discussion of individual changes. (Axel Kohlmeyer, Temple U) PR #2990, PR #2994, PR #3002
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #2973, PR #2975, PR #2976, PR #2977, PR #2983, PR #2985, PR #2989, PR #2991, PR #2993, PR #2998, PR #3003, PR #3004, PR #3007 , PR #3009

Backward compatibility notices:

• Most keywords that accept "yes/no" or "on/off" parameters will now accept "yes/no", "on/off", or "true/false" as valid arguments. This is not (yet) reflected in the manual. Some cases where there are more than just two choices have been adapted accordingly, but not all. Backward compatibility is retained. All tests pass.

Below is a list of major changes since the last stable release 29 October 2020

Same as the last time, this stable release contains over 4000 commits since the previous stable release. This includes many contributions from beyond the core LAMMPS developers, but also continues the internal refactoring of the code base to make it more consistent and reliable yet also take more advantage of C++ features where they help to simplify the code and easier to modify, maintain, and contribute to.

The LAMMPS homepage has been moved from https://lammps.sandia.gov to https://www.lammps.org which is now hosted at Temple U. This lifts bandwidth and access limitations and addresses some reliability issues.

General changes:

• Continued refactoring of the core LAMMPS code and many packages to increase code reuse, simplify new additions, improve consistentcy, and benefit from C++11 features. Several convenience functions and classes were added in the process.
• Reorganization of packages: the "USER" prefix has been dropped, some packages have prefixes to group them (CG-, DPD-, EXTRA-, ML-) and the contents of the USER-MISC package have been moved to appropriate existing or new packages. There are now EXTRA-PAIR, EXTRA-COMPUTE, EXTRA-FIX, EXTRA-DUMP, EXTRA-MOLECULE packages for the less commonly used styles. We recommend that external packages (i.e. those not included in the LAMMPS distribution) adopt a USER- prefix to make them recognizable as external package.
• Refactored multi-cutoff neighbor list support resulting in significant performance improvements for polydisperse granular systems.
• Continued improvements to the build systems, especially the CMake based version.
• Refactored the handling of embedded citation strings to make them more visible.
• Updates and additions to the programmer guide section of the manual including updated guidelines and information for contributing code to LAMMPS.
• Add support for using clang-format in the src tree with a configuration file and suitable comments in the source files. This is recommended for new contributions and will be gradually applied to existing .cpp files as the reformatting can interfere with the readability in some cases.
• Scripts to support building LAMMPS and its documentation via CMake on systems without direct internet access.

Updates and new commands or styles or packages:

• Expanded support for machine learning potentials in the ML-IAP package and the added ML-HDNNP, ML-PACE, ML-RANN packages
• New MDI package to allow client/server mode coupling of LAMMPS to other code using the MolSSI Driver Interface API
• New BROWNIAN package for Brownian dynamics time integration of point and extended particles plus updates for fix propel/self
• New DIELECTRIC package with boundary element solvers for computing induced charges at interfaces
• Major refactoring of the REAXFF package to eliminate dead code and inconsistencies, modernize force field file parsing, and correctly handle computing of the virial stress under different settings and with OpenMP
• Updates to the library interface and corresponding changes to the LAMMPS python module: bug fixes, additional introspection support and support for setting callbacks for fix external and other associated properties with C and Python callbacks/functions possible.
• Updated GPU package with improved support for OpenCL which enables using the GPU package with GPUs embedded in Intel processors (Iris, UHD, and HD graphics using the "NEO" OpenCL runtime).
• Diverse updates, performance improvements, and bugfixes for the following packages: DRUDE, PLUMED, COLVARS, KOKKOS, KIM, ML-IAP, SNAP, REACTION
• Many bugfixes, updates, and individual contributed commands and styles.

Backward compatibility notes:

• The LAMMPS python module is now a folder with multiple Python script files instead of a single lammps.py file. This should not affect how the module can be used "in-place" by setting environment variables. The python module contains a version check that should help detecting when a LAMMPS shared library that does not match the python module.
• Multi-cutoff neighbor list and communication is using a new and more flexible code path with a few additional constraints over the old code path, which is still available as a backup that must be explicitly requested.
• KIM package commands have been reorganized into a single wrapper and multiple sub-commands: kim_<something> has become kim <something>
• The CMake preset "minimal" has been renamed to "basic". There are no more "make yes/no-standard" and "make yes/no-user" due to the package reorganization; instead "make yes/no-basic" and a "make yes/no-most" targets have been added to reflect the corresponding CMake presets

This patch includes some final changes and bugfixes to create the stable release.

There are no substantial new features in this patch, only a variety of small updates and bug fixes for reported issues and based on extended testing with instrumented code and on platforms or with settings we do not run automatic tests for. Notable changes:

• bugfix for EAM/alloy pair style with KOKKOS on GPUs (Stan Moore, SNL) PR #2956
• bugfix for hybrid pair styles not enforcing a single pair_coeff statements for potentials that require it (Axel Kohlmeyer, Temple U) PR #2963
• logging of queried KIM collections locations with kim init (Ryan Elliott, UMN) PR #2949
• added section on parallel algorithms to manual adapted from new LAMMPS paper, PR #2917
• small bugfix for COLVARS package (Jerome Henin and Giacomo Fiorin) PR #2959
• small bugfix for handling of nevery keyword in fix bond/react (Jake Gissinger, NASA) PR #2969
• bugfix to neighbor list: prevent it from copying "unique" stencil/bin data (Stan Moore and Steve Plimpton, SNL) PR #2965
• updates to traditional make build system to enable C++11 compliance by default, list packages in alphabetical order and make package maintenance commands less verbose (Axel Kohlmeyer, Temple U) PR #2961
• collected small changes (Axel Kohlmeyer, Temple U) PR #2952, PR #2962, PR #2966
  • improved detection of double precision hardware with OpenCL and a workaround for neighbor list issues on sparse systems in the GPU package
  • improved C++ standard compliance for improved compatibility with compilers in C++20 mode
  • improved C library standard compliance by avoiding calling memset() and fwrite() with a null pointer
  • fix bug in traditional make build system support for ML-PACE package
  • add missing documentation for building with threaded FFTW3 support using non-standard library locations
  • plug memory leaks and compilation issue with 64-bit atom ids in MSCG package
  • avoid division by zero in fix dt/reset
  • fix portability issues and detect incompatibilities when compiling external libraries using CMake
  • prohibit KOKKOS from lowering the requested C++ standard

This is the release candidate for the next stable release. We will only accept urgent bugfixes and updates to documentation until then.
For people packaging stable LAMMPS releases into binary packages, please note that you have about one week left to submit any changes to LAMMPS where you have discovered issues related to building and packaging that we have overlooked. Once the stable release is out, you will have to maintain such changes as external patches until the next stable release or package a following patch release with those changes included.

Changes since the 31 August 2021 patch release:

• Updates and additions to the programmer guide section of the manual. Specifically, updated guidelines and information for contributing code to LAMMPS (Axel Kohlmeyer, Temple U) PR #2927
• Add new command line flag -skiprun testing input files for syntax error as this will skip main loops in run, minimize and similar commands PR #2919
• Avoid crashes when loading modules like NumPy multiple times into deleted/cleared LAMMPS instances. For that Py_Finalize() needs to be treated like MPI_Finalize() and thus called from main.cpp or a wrapper function in the library interface (Axel Kohlmeyer and Richard Berger, Temple U) PR #2923
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #2919, PR #2924, PR #2925, PR #2929, PR #2935, PR #2939, PR #2941

Changes since the 30 July 2021 patch release:

• Add KOKKOS accelerated styles for shear flow simulations with the nvt/sllod integrator (Emily Kahl, The University of Queensland) PR #2882
• New fix ttm/grid with improved file handling and distributed grid. The existing ttm fixes are refactored and modernized. This also generalizes and unbundles the grid communication class from the KSPACE package and thus updates all PPPM and MSM kspace style variants accordingly (Steve Plimpton, SNL) #2902
• New pair style coul/exclude to remove excluded Coulomb interactions to be used with kspace style scafacos for molecular systems (Axel Kohlmeyer, Temple U) PR #2886
• Add functionality to fix property/atom to support per-atom arrays in addition to per-atom vectors (Steve Plimpton SNL) PR #2342, PR #2889 PR #2903
• Update the COLVARS package to version 2021-08-06 (Giacomo Fiorin, NIH, and the colvars developers) PR #2863 and PR #2866
• Update to fix bond/swap to support a second kind of bond swapping model (Steve Plimpton, SNL) PR #2888
• File reader refactor, bug fixes, and unit tests for INTERLAYER package pair styles (Axel Kohlmeyer, Temple U) PR #2879, PR #2897
• Optimizations for SNAP with KOKKOS for large systems (enabled via config option) (Evan Weinberg, Nvidia) PR #2905
• Various updates and bugfixes for the KOKKOS package (Stan Moore, SNL) PR #2890, #2900
• Update factory functions to create or replace fixes and computes to return a pointer to the created class instance (Axel Kohlmeyer, Temple U) PR #2869
• Updates to the introductory pages of the LAMMPS documentation (Axel Kohlmeyer, Temple U) PR #2893
• Many small bug fixes, minor code improvements, and coding style, build system, documentation, formatting updates (multiple authors) PR #2804, PR #2862, PR #2861, PR #2865, PR #2868, PR #2876, PR #2880, PR #2881, PR #2885, PR #2887, PR #2889, PR #2891 , PR #2895, PR #2896, PR #2904, PR #2908, PR #2909, PR #2910, PR #2911, PR #2912, PR #2913, PR #2914

Backward compatibility notices:

• MC package fixes atom/swap, gcmc, widom, and charge/regulation were under some circumstances calling fixes that normally would be called at the "end_of_step()" stage during a time step instead in the "pre_exchange()" stage. This could lead to unexpected output or use of data from the previous time step (e.g. with fix print, fix ave/time etc.). These calls have been removed and the expected behavior has been restored.
• the output file format for the fix ttm electron temperature grid files has changed

Changes since the 28 July 2021 patch release:

This patch release contains a fix for a serious bug reported in issue #2858 that was present in LAMMPS since the 10 February 2021 patch release. We urge everybody that are using this version or any other versions released since then to upgrade to this patch release.

In addition, this patch release contains mostly minor code refactoring changes and a few fixes for issues were either a result of the recent package reorganization or were exposed by it. PR #2856, PR #2857, and PR #2860

Changes since the 2 July 2021 patch release:

• Completion of the package reorganization started in the 2 July 2021 release (Axel Kohlmeyer, Temple U) PR #2829
• Significant refactor of the REAXFF package and some updates to the QEQ package and corresponding code in the OPENMP and KOKKOS packages to have it better aligned with LAMMPS coding conventions, remove obsolete and dead code and implement missing features like support for compute stress/atom in the OpenMP version of the reaxff pair style. (Axel Kohlmeyer, Temple U, Aidan Thompson, SNL) PR #2708
• New fix pair/tracker and pair style tracker to track properties of pair interactions (Joel Clemmer, SNL) PR #2788
• New lammps_gather_bonds() function in the C library interface and corresponding Python module wrappers (Axel Kohlmeyer, Temple U, and Robert Meißner, TU Hamburg) PR #2850
• Updates to the CG-DNA package including a new atom style to address issues with tracking contact pairs (Oliver Henrich, Strathclyde U) PR #2827 and PR #2835
• Updates to the INTEL package to better support the new LLVM based Intel compilers and transition to use OpenMP pragmas for SIMD (Mike Brown, Intel) PR #2842 and PR #2849
• Add support for atom_modify map hash in the KOKKOS package (Stan Moore, SNL) PR #2815
• Updates to the C library interface and Python module to support all fix external functionality and make those behave more consistently, also document the calls (Axel Kohlmeyer, Temple U) PR #2837
• A new compute for the TALLY package to measure virial heat flow from one group of atoms to another (Donatas Surblys, Tohoku U) PR #2841
• Address issues and inconsistent behavior when using pair_modify nofdotr and compute stress/atom for pair styles in the MANYBODY and OPENMP packages. Add functionality to the unit tests to check for consistency in energy and global pressure (Axel Kohlmeyer, Temple U) PR #2736
• Various small bug fixes, coding style, build system, documentation and formatting updates (multiple authors) PR #2823, PR #2826, PR #2824, PR #2828, PR #2830, PR #2831, PR #2832, PR #2833, PR #2836, PR #2838, PR #2839, PR #2844, PR #2848, PR #2853, PR #2854, #2855

Backward compatibility notices:

• This patch release completes the package reorganization from the 2 July 2021 release. The USER-MISC package has been removed and its contents distributed to existing packages or one of the new packages INTERLAYER, ORIENT, EXTRA-COMPUTE, EXTRA-DUMP, EXTRA-FIX, EXTRA-MOLECULE, EXTRA-PAIR. Also some styles from MISC, MOLECULE and the src folder have been moved to more suitable packages. In case you are missing a style in your executable, LAMMPS should report which package contains the missing style and needs to be added.
• Some semantics of the fix external support functions to set global energy and virial have been changed to be more consistent.

Changes since the 27 May 2021 patch release:

• New package DIELECTRIC with boundary element solvers for computing induced charges at interfaces (Trung Nguyen and Monica Olvera del la Cruz, Northwestern) PR #2793
• New SO3 descriptor for the MLIAP package (Byungkyun Kang and Qiang Zhu, UNLV) PR #2796
• New fabric tensor compute (Joel Clemmer, SNL and Ishan Srivastava, LBL) PR #2795
• Variable pH support and bugfixes for Ewald self-energy in fix charge/regulation (Tine Curk, Northwestern) PR #2802
• Correctly handle KOKKOS package initialization with the library interface and the fact that the Kokkos library may only be initialized once (Stan Moore, SNL) PR #2470
• GPU package fixes for compilation with the ROCm/HIP backend (Richard Berger, Temple U) PR #2789
• Updates to Python package and examples (Richard Berger, Temple U) PR #2787
• Various small bug fixes, coding style, build system, documentation and formatting updates (multiple authors) PR #2786, PR #2790, PR #2798, #2803, #2810, #2813, #2817

Backward compatibility notes:

• The LAMMPS home page has been moved to https://www.lammps.org
• To reflect changes in the development process and the overall code quality we no longer differentiate between "standard" and "user packages. Thus many packages have been renamed. There are no more "user" packages included in LAMMPS except for USER-MISC. Also some packages have been renamed to better represent their content and also to group similar ones (e.g. machine learning or coarse grain or DPD packages). Some more reorganization of individual style files will follow in the next patch release.
• There is a new package (DPD-BASIC) and several dpd pair styles have been moved there from USER-MISC or the src folder.
• The "minimal.cmake" preset has been renamed to "basic.cmake" to match the corresponding "yes/no-basic" target in the conventional build and to avoid conflicts.