lammps

Changes since the 7 February 2024 release:

• New rebomos pair style for MoS2 which was provided as external source for over a decade (multiple authors see PR) PR #4087
• New fix wall/flow command which provides flow boundary conditions (Vladislav Galigerov, Higher School of Economics and Daniil Pavlov, The Moscow Institute of Physics and Technology) PR #4069
• New fix deform/pressure command for expanded deformation controls specifically aimed at mesoscopic and discrete element models (Joel Clemmer, SNL and Kevin Hanley, U. Edinburgh and Jose Salomon, Imperial College) PR #4017
• New angle and dihedral styles cosine/squared/restricted for use with the MARTINI force field (Evangelos Voyiatzis) PR #4113
• New pair style pedone for the non-Coulomb part of the Pedone (PMMCS) potential (Axel Kohlmeyer, Temple U) PR #4129
• Small updates for the ELECTRODE package (new qtotal, eta keywords, check for mobile atoms) (Ludwig Ahrense-Iwers, Robert Meissner, TU Hamburg, Shern Tee, Griffith U.) PR #4095
• Small updates to fix pimd/langevin to improve the support for the pimd method (Yifan Li, Princeton) PR #4107
• Improve sorting performance for Kokkos with GPUs and address (Stan Moore, SNL), PR #4127
• Update bundled Kokkos library to version 4.3.00 (Stan Moore, SNL and the Kokkos developers) PR #4096, PR #4124
• Add option to package command that selects building the atom map on the CPU instead of the GPU device. This can lead to significant speedups for runs of large molecular systems (billions of molecules) with a very large number of MPI ranks (> 1000) during initialization (up to 100x at 4096 ranks) and during the run (up to 2x with 4096 ranks) (Stan Moore, SNL) PR #4079
• Add support for general triclinic simulation boxes and systems (Steve Plimpton) PR #3984
• Add support for ACE descriptors to the ML-IAP package (James Goff, SNL) PR #4078
• Add support for a conical shape to fix indent (Evangelos Voyiatzis, NovaMechanics Ltd) PR #3989
• Many small bug fixes, minor code improvements and refactoring, and updates for coding style, build system, documentation, and formatting (multiple authors) PR #4074, PR #4080, PR #4082, PR #4084, PR #4085, PR #4086, PR #4088, PR #4089, PR #4090, PR #4091, PR #4094, PR #4097, PR #4098, PR #4099, PR #4108, PR #4101, PR #4102, PR #4103, PR #4105, PR #4111, PR #4116, PR #4120, PR #4121, PR #4122, PR #4123, PR #4125, PR #4126, PR #4130, PR #4134, PR #4135, PR #4139

Backward compatibility notes:

• The zlo, zhi value of a box for a 2d system may no longer be exactly zero. zlo must be less than zero, zhi must be greater.
• The dump style custom/cfg/yaml etc. keywords "temperature" and "heatflow" are no longer available directly, they must be accessed via compute property/atom now (like other atom style properties)

This is the third update to the 2 August 2023 stable release that fixes bugs that have been reported since then and updates some libraries, dependencies, tools, and build system support.

The following individual changes are included:

• correct factor of 2 force error in angle style cosine/periodic for multiplicity 1
• avoid 32-bit integer overflow when running simulations of large systems requiring -DLAMMPS_BIGBIG with PPPM and SHAKE
• fix bug when using "unpack_exchange()" with KOKKOS on device
• fix bug in fix style neb which was not always creating the rootworld communicator when needed
• fix bug in neb command where the print verbosity was not initialized
• fix bugs in fix style bond/react backported from PR #3905
• fix bugs in pairstyle meam/ms for non-zero t1m parameter settings and incorrect use of the ialloy parameter.
• fix scaling bug in compute xrd when using radians as input
• error out if fixes gcmc, sgcmc, widom, charge regulation and pair style dscmc are used without per-type masses
• flag that INTEL package is incompatible with run style verlet/split
• make fix cmap compatible with output from charmm-gui which does not create complete cmap parameter files
• gracefully handle reaxff parameter files without hydrogen bond parameters
• update references to (no longer available) fix ave/spatial with correct alternatives
• avoid initializing mliappy multiple times
• allow use of QEQ fixes with GPU package (must explicitly set newton on, though)
• use better detection and application of cuFFT library for KOKKOS with CMake builds
• correct compilation settings for compiling ML-QUIP package correctly with CMake
• export symbols from executable when building with a static LAMMPS library so they can be accessed by plugins

This update addresses some compilation issues using CMake with the 7 February 2024 version that only happen with custom compilations for some unusual combination of LAMMPS packages (hence the issue was not detected by our automated integration testing).
The only pull request included is #4077. There are no functional changes, so the binary packages attached to the 7 February 2024 feature release do not need to be rebuilt for this update.

Changes since the 21 November 2023 release:

• New compute pace command for evaluating ACE descriptors which functions similar to compute snap (James Goff, Drew Rohskopf, Aidan Thompson SNL) PR #3869
• New "ternary()" function for variables (Steve Plimpton) PR #3987
• Add support for direct references to variable functions for custom properties introduced with fix properties/atom (Steve Plimpton) PR #3990
• New compute to identify under-coordinated particles (rattlers) and a new fix to measure the nonaffine displacement of particles (Joel Clemmer, SNL) PR #3858
• New compute reaxff/atom to get access to local bond information for ReaxFF (Richard Berger, LANL) PR #3938
• Add feature to compute sna/atom to use a fixed number of neighbors, and a new compute slcsa/atom for supervised learning structural analysis, (Paul Lafourcade, CEA) PR #3996
• add ZBL core-repulsion to ML-PACE, automatic conversion of supported potential file formats (Yury Lysogorskiy, RUB) PR #3985
• Several new pair styles for the GPU package including coul/long/slater/gpu (Trung Nguyen, U Chicago) PR #4009
• Add KOKKOS package versions of fix temp/rescale and fix temp/berendsen (Stan Moore, SNL) PR #4012
• Add KOKKOS package versions of pair style lj/charmmfsw/coul/long and dihedral style charmmfsw, (Mitch Murphy) PR #4030
• Add support for heFFTe library to do FFTs (Miroslav Stoyanov, ORNL) PR #3963
• Decouple defines for the FFT libraries for regular and KOKKOS 3d-FFT support, add displaying FFT information with info and lmp -h (Nick Hagerty, ORNL and Axel Kohlmeyer, Temple U) PR #4007
• Updates for multiple INTERLAYER potential files and bugfixes for a couple of pair styles (Wengen Ouyang, Wuhan University) PR #4025 and PR #4029
• Update of the bundled linear algebra library to the state of LAPACK 3.12.0 (Axel Kohlmeyer, Temple U) PR #3992
• Update of the bundled fmtlib sources to version 10.2.1 (Axel Kohlmeyer, Temple U) PR #4042
• Update the bundled Kokkos library to version 4.2.0 (Stan Moore, SNL, and the Kokkos developers) PR #3983
• ML-PACE pair style optimizations for KOKKOS with GPUs (Stan Moore, SNL) PR #4031
• Use C++ templating to reduce the number of NPair and NStencil classes and improve code re-use (Joel Clemmer, SNL) PR #3430
• Add Born matrix support to more potentials & inclusion of angle and dihedral contribution to compuite stress/mop and stress/mop/profile (Evangelos Voyiatzis, NovaMechanics Ltd.) PR #3833
• HowTo tutorial for using Moltemplate (Otello Roscioni, MaterialX Ltd), PR #4002
• Add support for a "Dipoles" section to molecule files (Axel Kohlmeyer, Temple U) PR #4046
• Add fix numdiff based tests to the force style testers in the unittest tree (Axel Kohlmeyer, Temple U) PR #4041
• Many small bug fixes, minor code improvements and refactoring, and updates for coding style, build system, documentation, and formatting (multiple authors) PR #3905, PR #3962, PR #3988, PR #3993, PR #3997, PR #3998, PR #4000, PR #4001, PR #4003, PR #4004, PR #4005, PR #4006, PR #4011, PR #4015, PR #4018, PR #4021, PR #4022, PR #4023, PR #4034, PR #4036, PR #4037, PR #4039, PR #4040, PR #4047, PR #4048, PR #4051, PR #4054, PR #4058, PR #4062, PR #4063, PR #4067, PR #4070, PR #4072

Backward compatibility notes:

• The "reax/c" alias to provide backward compatibility for "reaxff" commands and keywords has been (finally) removed. Now using "reaxff" is required.
• The format of binary restart files has changed in an incompatible way for cases where bond style lepton or angle style lepton are used.

This is the second update to the 2 August 2023 stable release that fixes bugs that have been reported since then and updates some libraries, dependencies, tools, and build system support.

The following individual changes are included:

• enforce consistent OpenMP threads settings for /omp styles (avoids crashes and memory corruption)
• accept very old style ReaxFF force field that are missing the ovc property for bonds and set it to 0.0 (it is 0.0 most of the time anyway)
• avoid segfaults when querying LAMMPS for thermo data before the Thermo class has been instantiated
• identify Windows 11 23H2
• bugfix to ellipsoid region for correct forces with fix wall/region
• bugfix and updates to computes cluster/atom, aggregate/atom, and fragment/atom to add missing communication of ghost atoms and to avoid deadlocks
• fix cut-n-paste type in minimize style error message
• update CWD in LAMMPS GUI also when saving a buffer
• fix bug in LAMMPS GUI where the number of threads could not be increased
• fix delete/delete[] mismatch in LAMMPS GUI
• check LAMMPS library loaded as plugin to be compatible with LAMMPS GUI
• bugfix for neighbor list trimming on requests that request neighbors of ghosts
• properly quote keywords containing special characters in dump yaml output
• detect more cases of inconsistent KOKKOS style usage and error out gracefully
• add sanity check to python/install.py file and improve readability of error messages
• if tools/phonon/phana uses linalg, make sure it is built before linking
• nullify deleted pointers when creating styles in Force or Update since the creation may fail and trigger an exception and the we may run into a double free error crashing the application
• avoid "invalid escape" warning with python 3.12
• fix bug in fix pimd/langevin
• make certain that generated argv lists are NULL terminated to avoid segfaults with OpenMPI 5.x and later
• fix bug in pace/extrapolate
• fix bug in the rigid fixes that was causing a drift in the z-coordinate with 2d systems
• fix bugs in fix mvv/* compatibility checks
• restore using nvcc_wrapper with kokkos_cuda.cmake preset
• fix memory leak in dump style image and remove redundant code
• the scale yes option is not supported with fix adapt/fep for atom charges and diameters, update list of supported pair styles, fix bug with global scale factor
• Avoid segfault in fix atom/swap for systems without per-type masses. Warn if both per-type and per-atom masses are set that per-type masses will be used
• correct DPI settings in mesh images for compute saed and compute xrd so the images display correctly in PDF files
• avoid copying over terminating null byte in balance and fix balance shift keyword
• may only check for region inside box in fix gcmc and fix widom if the region keyword was used
• avoid deprecated python initialization for python 3.12 and later
• avoid warnings from including multiple cython generated include files
• add valgrind suppresions for MPICH

Changes since the 2 August 2023 release:

• New per-atom compute to calculate local atom type compositions (Megan McCarthy, SNL) PR #3871
• New fix press/langevin command for a langevin based barostat (Germain Claview, TU Eindhoven) PR #3791
• New pair style nb3b/screened which computes a screened angle interactions compared to nb3b/harmonic (Federica Lodesani, University of Modena) PR #3960
• New snap/intel pair style implementing AVX512 vectorization for use with Intel compiler and x86 CPUs (Mike Brown, Intel) PR #3921 3921
• Add support for numerical integrators without normal mode transformation to fix pimd/langevin (mode pimd). (Yifan Li, Princeton University) PR #3970
• New KOKKOS versions of fix efield, fix spring/self, and pair style yukawa/colloid (Trung Nguyen, U Chicago) PR #3909
• Update the bundled Kokkos library to version 4.1.0 (Stan Moore, SNL, and the Kokkos developers) PR #3670
• Honor neighbor list "trim" options for skip lists (Stan Moore, SNL) PR #3974
• Check for CUDA/ROCm aware OpenMPI installation dynamically for use with Kokkos (Vladislav Galigerov, Higher School of Economics, Russia) PR #3828
• Update the bundled libfmt code to version 10.1.1 (Axel Kohlmeyer, TempleU, and the libfmt developers) PR #3832, PR #3884, and PR #3906
• add option to do anti-aliasing for better image quality with dump image and dump movie (Axel Kohlmeyer, Temple U), PR #3889
• Raise the CMake version requirement to 3.16 and removed workarounds for older versions (Axel Kohlmeyer, Temple U) PR #3836
• The -DLAMMPS_EXCEPTIONS setting is now always active (Axel Kohlmeyer, Temple U) PR #3736
• Remove obsolete MSCG package (Axel Kohlmeyer, Temple U) PR #3856
• Remove unmaintained MPIIO package which causes crashes (Axel Kohlmeyer, Temple U) PR #3894
• Refactoring of handing of references to computes and fixes to consistently index global and per-atom properties. (Steve Plimpton) PR #3896
• Multiple bug fixes, improvements, and added features for the LAMMPS GUI updating it to version 1.5 (Axel Kohlmeyer, Temple U) PR #3883, PR #3890, PR #3893, PR #3904, PR #3910, PR #3912, PR #3923
• Many small bug fixes, minor code improvements and refactoring, and updates for coding style, build system, documentation, and formatting (multiple authors) PR #3724, PR #3846, PR #3867, PR #3881, PR #3885, PR #3887, PR #3888, PR #3892, PR #3898, PR #3900, PR #3903, PR #3905, PR #3908, PR #3911, PR #3914, PR #3915, PR #3922, PR #3924, PR #3930, PR #3931, PR #3937, PR #3941, PR #3943, PR #3944, PR #3947, PR #3948, PR #3949, PR #3950, PR #3953, PR #3954, PR #3957, PR #3958, PR #3964, PR #3966, PR #3968, PR #3971, PR #3973, PR #3975, PR #3976, PR #3979, PR #3981

Backward compatibility notes:

• The MSCG package and thus fix mscg has been removed
• The MPIIO package has been removed. The corresponding dump styles are no longer available and .mpiio restarts cannot be read anymore
• CMake version 3.16 or later is now required to build LAMMPS with CMake
• A C++17 capable compiler is now required to compile the KOKKOS package
• using a triclinic simulation cell now requires atom IDs due to changes in the neighbor list build algorithms
• the refactoring of variable access to compute and fix data has the following consequences:
  • the compute voronoi/atom peratom option was dropped; it now always produces peratom data. The local option is now used to also generate local data
  • an inputs option was added to compute reduce to operation on peratom (default) or local data. You must use it to operate on local data
  • the rules for equal, vector, atom-style variables changed a bit for how they access output from computes and fixes. An equal-style variable can access any kind of data, using C_ID, instead of c_ID (similar for fixes) to access per-atom data instead of global data.
  • vector and atom-style varaiables can only access global vector and per-atom data directly. They can use an equal-style variable to access other kinds of data indirectly.

This is an update to the 2 August 2023 stable release that fixes bugs that have been reported since then and updates some libraries, dependencies, tools, and build system support.

The following individual changes are included:

• avoid compilation failures for PYTHON package with legacy build system on Linux systems that have only python3-config and no python-config like Debian or Ubuntu
• bugfix for pair style dpd/gpu
• make pair style awpmd compatible with C++17 compilers
• disable testing for (broken) MPIIO package features
• bugfix for compute global/atom
• bugfixes for fix srd
• bugfix for mdi
• fix bug in create_atoms mesh to recognize files starting with solid binary as binary, do not require a lattice, and plug memory leak
• fix bug in Kokkos ReaxFF on GPUs when border communication is done by host
• fix multiple initialization bug in custom/adios dump style
• avoid uninitialized data access in colvars library
• do not restore Atom::map_user from restart files and allow to override the map style with binary restart
• fix element mapping bug in pair style hdnnp when used as a hybrid sub-style
• the MESONT package depends on the MOLECULE package
• correct link to Kokkos compatibility info
• make hipfft support compatible with ROCm 6.0 and later
• replace leftover references to lib/smd and smd to use lib/machdyn and machdyn
• updates to sync lammps-shell's internal tables with the current state of LAMMPS
• corrections for compiling tools with GNU make and improve documentation when using CMake to build them
• remove some leftover temporary files created by unit tests
• cmake updates and corrections
• documentation corrections
• corrected clang-format detection for Debian Linux
• update lammps-gui to version 1.2 with bugfixes and enhancements

Below is a list of major changes since the last stable release 23 June 2022

This stable release adds about 5500 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.

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.
• Continued improving of error message to be more specific and provide more hints about what went wrong
• Enhancements and extensions of the Programmer' Guide section of the manual. For example more information about programming conventions, a detailed example for writing pair styles from scratch, information about porting code for old LAMMPS versions to the current development version

Updates and new commands or styles or packages:

• New AMOEBA package implementing the Amoeba and Hippo force fields (including GPU support)
• New ML-POD package for machine learning potentials using "proper orthogonal descriptors"
• New LEPTON package for defining the energy/forces for pair styles and fixes from text strings with analytical expressions
• Basic support for symbolic types aka type labels
• New LAMMPS GUI tool, a simple graphical text editor for input files with LAMMPS built in so the input can be run without a LAMMPS executable
• New command reset_atoms that serves as a front end for reset_atom_ids, reset_mol_ids and the new reset_atoms image for reducing the value of image flags
• New angle_write and dihedral_write commands to produce table files for use with the corresponding table styles
• Replace overzealous checks that lead to "Compute not current" errors with more forgiving checks
• Add support for setting and outputting vector style variables with a python-list-like format
• Enhancements for PyLammps
• New compute efield/wolf/atom command to approximate local electrical field for individual atoms
• New fix scgmc command imported from the external USER-VCSGC package
• New features and updates to the ELECTRODE package
• Port of more fixes and pair styles to the KOKKOS package, most notably the MEAM and ML-IAP packages
• Updates and bugfixes to the DIELECTRIC package
• Update COLVARS package to version 2023-05-01
• Improvements to the MDI package with more functionality
• Updates and refactoring of the GRANULAR package to make it more consistent and flexible
• Updates to the ML-PACE package
• CG-SDK package was rename to CG-SPICA and some enhancements added
• The bundled linalg library (a subset of LAPACK and BLAS) was converted from Fortran to C++ so LAMMPS can be more easily compiled on platforms that do not have a Fortran compiler or a ready-to-use BLAS/LAPACK installation
• Update bundled Kokkos library to version 3.7.2
• Update bundled fmtlib files to version 9.1.0
• New fix pair command to access per-atom data computed by pair styles
• New pair styles xlz and born/gauss
• New fix pimd/langevin for path-integral simulations using a Langevin thermostat
• New fix alchemy and compute pressure/alchemy commands for multi-partition alchemical transformations
• New bond style harmonic/restrain to restrain bonds to their current length
• New pair styles lj/cut/sphere, lj/expand/sphere, and lepton/sphere which use the individual particle diameter from atom style sphere as a potential property instead of a per-type pair_coeff setting
• New pair style aip/water/2dm for interfaces between water and 2d materials
• Support more pair, bond, and angle styles with compute born/matrix
• Updates, enhancements, and bugfixes for the BPM package
• Multiple bugfixes and enhancements for the INTEL package
• Add unified Python interface for ML-IAP package including Kokkos support
• Support using fix shake and fix rattle during minimization. The constraints are replaced by strong restraint forces
• Update of pair style mesocnt to include all functionality and some additions over the corresponding fortran versions. The latter are thus obsolete and were removed.
• Updates to the LAMMPS Fortran module. This is now complete and thus the obsolete older modules/wrappers were removed since they were in need of updating.
• Various GPU package improvements and bug fixes
• Refactoring of distributed grids making some of that data also accessible for computes and dumps

Backward compatibility notices:

• The CG-SDK package is now called CG-SPICA
• The LATTE package and fix latter are removed. Its functionality is provided by the MDI package
• the default setting for neighbor list rebuilds has been changed from delay 10 to delay 0
• Unlike other variables, atomfile style variables are now deleted with the clear command
• The internal fix STORE command has been split into fix STORE/GLOBAL and fix STORE/PERATOM
• Obsolete Fortran interfaces to the LAMMPS C-library interface were removed
• fix pimd was renamed to fix pimd/nvt
• pair style mesont/tpm, compute style mesont, and atom style mesont were removed
• make install in a CMake based installation will no longer install the LAMMPS python module. make install-python can be used for that.

This release primarily contains bug fixes for the 15 June 2023 feature release to make this a stable release.

Changes since the 15 June 2023 release:

• Remove obsolete Fortran interfaces (Axel Kohlmeyer, Temple U) PR #3825
• LAMMPS GUI, a simple graphical text editor with LAMMPS built in (Axel Kohlmeyer, Temple U) PR #3870
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3814, PR #3819, PR #3821, PR #3822, PR #3823, PR #3826, PR #3827, PR #3829, PR #3830, PR #3834, PR #3839, PR #3842, PR #3843, PR #3844, PR #3845, PR #3848, PR #3849, PR #3850, PR #3851, PR #3855, PR #3859, PR #3860, PR #3861, PR #3864, PR #3865, PR #3874

Changes since the 28 March 2023 release:

• The LATTE package was removed as it is superseded by the MDI package which provides a more generic interface to couple to quantum codes (Steve Plimpton) PR #3716
• Updates to fix mdi/qm and fix mdi/qmmm to be compatible with quantum codes that do not support periodic boundaries (Taylor Banes, MolSSI) PR #3727
• Update COLVARS package to version 2023-05-01 (Giacomo Fiorin, NIH and Colvars developers) PR #3783
• Update bundled Kokkos library to version 3.7.2 (Stan Moore, SNL, and the Kokkos developers) PR #3806
• Add support for exchange communication for fixes to KOKKOS, this can provide significant speedups for certain simulations using GPUs (Stan Moore, SNL, based on work by Denis Taniguchi, Newcastle University) PR #1394
• Multiple performance optimization for KOKKOS package with GPUs (Stan Moore, SNL):
  • Add support for performing the spatial sorting of atoms on GPU devices, PR #3740
  • Fuse some Kokkos kernels to reduce launch latency for small systems, PR #3758
  • Compute atom map (including hash style) on GPU devices, PR #3769
• New pair styles lj/cut/sphere, lj/expand/sphere, and lepton/sphere which use the individual particle diameter from atom style sphere as a potential property instead of a per-type pair_coeff setting (Axel Kohlmeyer, Temple U) PR #3714
• New pair style aip/water/2dm for interfaces between water and 2d materials (Wengen Ouyang, Wuhan University), optimized versions by (Xiaohui Duan, Shandong University, and Ping Gao ,National Supercomputing Center in Wuxi) PR #3787
• New compute count/type command to efficiently count number of atoms or bonds of given types (Steve Plimpton) PR #3761
• New fix pimd/langevin for path-integral simulations using a Langevin thermostat (instead of a massive Nose-Hoover) (Yifan Li, Princeton) PR #3660
• Add support for setting and outputting vector style variables with a python-list-like format (Steve Plimpton) PR #3767
• Add support for fix adapt to pair style kim (global scale factor only) (Ilia Nikiforov, U of Minnesota) PR #3777
• Add support for bond and angle style contributions to compute stress/mop and compute stress/mop/profile (Evangelos Voyiatzis, NovaMechanics Ltd) PR #3792
• Add support for bond style forces to compute stress/cartesian (Lars Veldscholte, University of Twente) PR #3797
• Multiple bugfixes and enhancements for the INTEL package (Mike Brown, Intel) PR #3812
• Enhancements for PyLammps (Richard Berger, LANL) PR #3811
• Replace overzealous checks that lead to "Compute not current" errors with more forgiving checks. (Steve Plimpton) PR #3771
• Update of phonon tool (phana) with upstream version, add CMake support and include libraries (Axel Kohlmeyer, Temple U) PR #3762
• Update of the LAMMPS theme for the documentation to be compatible with Sphinx 6.x and 7.x (Richard Berger, LANL) PR #3747
• Reorganization and updates of the "Modifying and extending LAMMPS" section of the programmer's guide (Joel Clemmer, SNL), PR #3755
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3632, PR #3717, PR #3718, PR #3719, PR #3720, PR #3722, PR #3723, PR #3725, PR #3726, PR #3728, PR #3729, PR #3731, PR #3733, PR #3734, PR #3735, PR #3737, PR #3738, PR #3739, PR #3744, PR #3745, PR #3746, PR #3753, PR #3754, PR #3756, PR #3763, PR #3766, PR #3768, PR #3770, PR #3776, PR #3779, PR #3780, PR #3781, PR #3790, PR #3793, PR #3795, PR #3800, PR #3802, PR #3803, PR #3804, PR #3807, PR #3809, PR #3815, PR #3816, PR #3817

Backward compatibility notes:

• The LATTE package and fix latte command are no longer available

This is an update to the 23 June 2022 stable release that fixes bugs that have been reported since then and updates some libraries, dependencies, and build system support.

The following individual changes are included:

• compilation fix for bundled Kokkos lib on Fedora 38
• expose GPU debugging for GPU package to CMake build
• update external MSCG library to snapshot with included important bugfix
• allow building PLUMED package with MinGW64 Linux-to-Windows cross-compilers
• small corrections for the manual
• remove obsolete (and previously optional) constructor argument required for compatibility with recent ADIOS2 versions
• bugfix for ndx2group command to avoid crash when no atom map is available
• allow fix oneway to be used with dynamic groups
• update fix property/atom/kk to be compatible with non-kokkos version
• installing/removing the MDI package requires recompilation of main.cpp
• fix bug to correct force computation in fix wall/morse, update its unit test
• synchronize fmt::format code with develop branch to increase portability with Nvidia compilers
• correct Error API for functions supporting variable arguments as needed by fmt::format upgrade
• no need to store topology information with ghost atoms
• fix bug with "ids once" option for compute chunk/atom
• fix a few bugs in the INTEL package (32-bit integer overflow with neighbor lists, missing initializer for dihedral style charmm, calling double precision math functions in floating point precision templated classes, plug memory leak in Nose-Hoover styles)
• avoid segmentation fault with atom style edpd

This is a tiny update for the 28 March 2023 release that changes the Sphinx setting to address a problem updating the online documentation. There are no functional changes.

Changes since the 8 February 2023 release:

• Support more pair, bond, and angle styles with compute born/matrix (Evangelos Voyiatzis) PR #3650, PR #3655, PR #3668
• Refactor of the GRANULAR package to make it more modular and features more easily reusable (Joel Clemmer and Dan Bolintineanu, SNL) PR #3512
• New fix wall/lepton and wall/table for custom wall potentials (Axel Kohlmeyer, Temple U) PR #3657
• New bond style harmonic/restrain to restrain bonds to their current length (Axel Kohlmeyer, Temple U) PR #3671
• New fix alchemy and compute pressure/alchemy commands for multi-partition alchemical transformations (Axel Kohlmeyer, Temple U) PR #3662
• New fix mdi/qmmm style and examples for coupling LAMMPS to quantum codes (PySCF, NWChem, LATTE) via MDI for QM/MM simulations (Steve Plimpton) PR #3628
• GPU package performance improvements (Mike Brown, Intel) PR #3675
• New option "sort yes/no" for balance and fix balance (Steve Plimpton) PR #3677
• Small updates and fixes for the BPM package and related items (Joel Clemmer) PR #3696
• New pair style born/gauss which is used as example in new programmer's guide section on developing pair styles (Axel Kohlmeyer, Temple U), PR #3667
• Refactor per-chunk compute styles to use a common base class and thus reduce replicated code, (Axel Kohlmeyer, Temple U), PR #3691
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3643, PR #3644, PR #3648, PR #3649, PR #3651, PR #3653, PR #3656, PR #3658, PR #3659, PR #3661, PR #3663, PR #3664, PR #3666, PR #3669, PR #3672, PR #3674, PR #3676, PR #3679, PR #3680, PR #3681, PR #3684, PR #3687, PR #3689, PR #3693, PR #3694, PR #3695, PR #3698, PR #3699, PR #3701, PR #3702, PR #3703, PR #3705, PR #3709, PR #3712

Backward compatibility notes:

• Pair style gauss now honors the special_bonds lj settings
• make install in a CMake based installation will no longer install the LAMMPS python module. make install-python can be used for that.

This is an update to the 23 June 2022 stable release that fixes a bugs that have been reported since then and updates some libraries, dependencies, and build system support.

The following individual fixes and changes are included (also see PR #3593 and PR #3595):

• updates and corrections for package settings handling with traditional make build system
• synchronize GitHub related settings and file with upstream
• update LAMMPS developer contact info in source code (see #3595)
• update sphinx settings and theme files to what is used with upstream (see #3595)
• synchronize the documentation with upstream where applicable
• provide fallback URLs for external libraries to cached copies on download.lammps.org when automatic download from primary source fails or checksum does not match
• support compilation of ADIOS package without MPI
• update n2p2 library for ML-HDNNP package
• fix typo in meam/spline/sw potential file
• bugfix for checking on valid numbers with utils::*numeric() functions
• bugfix for DPD styles when used with special bond factors that are not 0 or 1
• bugfix for stress tally with dihedral style table
• pair style wf does not support pair modify shift by construction
• bugfix for minimization with fix box/relax and KOKKOS
• bugfix for neighbor list build with KOKKOS
• bugfixes for memory leaks in KOKKOS
• bugfixes for using hybrid pair styles with KOKKOS
• bugfixes for multiple GPU tag issues in KOKKOS styles
• bugfix for bond/angle style gaussian that had prematurely truncated the potential
• bugfix for argument parsing with pair styles nm/cut/coul/cut and nm/cut/coul/long
• bugfix for traditional make build where some package settings were not removed when uninstalling
• bugfix for TIP4P styles where sometimes an H atom is not found if its O atom is a ghost
• bugfix for checking region extent in triclinic boxes with fix gcmc and fix widom
• bugfixes for fix pimd
• bugfixes for pair style gauss with GPU package, make special_bonds handling consistent across all variants (see PR #3644)
• remove memory leaks for examples/COUPLE codes
• fix portability issues for compiling LAMMPS on Solaris/OpenIndiana
• fix portability issues for compiling LAMMPS using musl-libc instead of GNU libc
• add compatibility for compiling the GPU package with CUDA 12.0 (the included Kokkos library is not ported and optimized for CUDA 12.0 a newer LAMMPS feature release that included Kokkos 3.7.1 or later is required for that)
• updates and bugfixes for library interface wrapper that allows loading LAMMPS as a plugin library at runtime

Backward compatibility notice:

• pair style gauss now honors the special_bonds settings

Changes since the 22 December 2022 release:

• Port of the AMOEBA package code to the GPU package (Trung Nguyen, U Chicago) PR #3599
• Update the bundled Kokkos library to version 3.7.1 and some related code improvements also for upcoming changes in Kokkos 4.0 (Stan Moore and Christian Trott, SNL) PR #3532 and PR #3568
• Port of pace/extrapolation pair style to KOKKOS (Yury Lysogorskiy (ICAMS, RUB) PR #3585, PR #3629
• Port of pair styles lj/expand/coul/long and lj/cut/dipole/cut and atom style dipole to KOKKOS (Trung Nguyen, U Chicago) PR #3623
• Port of the ML-IAP Python interface for PyTorch to KOKKOS (Matt Bettencourt, NVIDIA) PR #3577, PR #3606
• New pair style meam/ms implementing the multi-state MEAM extension including port to KOKKOS (Drew Rohskopf and
  Aidan Thompson, SNL, and Mike Baskes, LANL, UNT) PR #3608
• Converted "linalg" library from Fortran to C++ so that no longer a Fortran compiler is required if a package requires BLAS/LAPACK and no suitable library is present (Axel Kohlmeyer, Temple U) PR #3579
• Remove mesont/tpm pair style and related styles as well as the corresponding Fortran library from MESONT package as they are superseded by the mesocnt pair and bond/angle styles. (Axel Kohlmeyer, Temple U) PR #3605
• New LEPTON package that allows custom potential functions through evaluating expressions provided as string through the Lepton library written originally for OpenMM (Axel Kohlmeyer, Temple U) PR #3571, PR #3590
• New angle_write and dihedral_write commands (Axel Kohlmeyer, Temple U) PR #3573
• New compute efield/wolf/atom command that can approximate the electrostatic field at atom positions using Wolf summation (Axel Kohlmeyer, Temple U) PR #3551
• Bugfix for DPD-BASIC pair styles and their accelerated versions when used with bonds and special_bonds factors that are not 0 or 1. (Axel Kohlmeyer, Temple U) PR #3575
• Updates to the DIELECTRIC package that reverses the logic of how to store original and scaled charges and thus results in more consistent behavior of computes and fixes outside the DIELECTRIC package (Trung Nguyen, UChicago) PR #3576
• Support for ABC-FIRE variant of FIRE minimizer (Sebastian Echeverri Restrepo, King's College London) PR #3591, PR #3594
• Support for "equal" mode of NEB (Tom D Swinburne, CNRS), PR #3596
• Additional functions to access topology data in the C-library interface with support in all derived wrappers and interfaces (Evangelos Voyiatzis) PR #3614
• Fall back to download external libraries from download.lammps.org instead of their original location in case that server is unavailable, the URL changed or the checksum changed (Axel Kohlmeyer, Temple U) PR #3630
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3561, PR #3569, PR #3570, PR #3572, PR #3574, PR #3581, PR #3582, PR #3587, PR #3588, PR #3589, PR #3592, PR #3597, PR #3598, PR #3601, PR #3602, PR #3603, PR #3604, PR #3607, PR #3610, PR #3613, PR #3615, PR #3617, PR #3620, PR #3621, PR #3624, PR #3631, PR #3635, PR #3636, PR #3637, PR #3638

Backward compatibility notes:

• the obsolete legacy Fortran 77 wrapper for the LAMMPS library interface has been removed from examples/COUPLE
• the obsolete fire/old variant of the FIRE minimizer was removed
• pair style mesont/tpm, compute style mesont, and atom style mesont were removed

Changes since the 3 November 2022 release:

• new package ML-POD with a pair style for machine learning potentials using "proper orthogonal descriptors" (POD) and a command for training (Ngoc Cuong Nguyen, MIT and Andrew Rohskopf, SNL) PR #3449
• new command reset_atoms that is a front end for reset_atom_ids and reset_mol_ids and the new sub-command reset_atoms image to reset image flags consistently for molecule fragments (Axel Kohlmeyer, Temple U) PR #3530
• new features and updates to the ELECTRODE package (Ludwig Ahrens-Iwers and Robert Meißner, Hamburg U of T and Shern Tee, U of Queensland) PR #3544
• new fix sgcmc command in the MC package imported from the external USER-VCSGC package (Aidan Thompson, SNL and Axel Kohlmeyer, Temple U) PR #3556
• add KOKKOS versions of fix viscous and fix dt/reset (Michal Kanksi, Jagiellonian University) PR #3522
• refactored distributed grids code to be more general and add new commands that can access those grids or compute/process/output grid properties (Steve Plimpton) PR #3405
• new Python classes and functions to build tables for pair style, bond style, angle style, and dihedral style table (Axel Kohlmeyer, Temple U) PR #3559
• updates, bugfixes, and a few new features for fix bond/react (Jake Gissinger, NASA Langley) PR #3514
• some more updates to the LAMMPS Fortran interface module (Karl Hammond, U of Missouri) PR #3547
• remove style suffixes when writing binary restart files allowing to restart non-accelerated runs from accelerated runs (Axel Kohlmeyer, Temple U and Stan Moore, SNL) PR #3538
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3516, PR #3517, PR #3521, PR #3524, PR #3525, PR #3527, PR #3529, PR #3533, PR #3534, PR #3539, PR #3541, PR #3548, PR #3550, PR #3552, PR #3553, PR #3555, PR #3558, PR #3560, PR #3562, PR #3566

Backward compatibility notices:

• The checks for valid floating-point and integer numbers have been improved and are more strict now. This can lead to old inputs failing because of invalid numbers
• The Si.b.meam.sw.spline had to be corrected for an invalid floating-point number (see previous note. here the "e" in the exponent was missing and thus the exponent was incorrectly ignored). Most calculations, but not all, will be unaffected since this only concerned the spline coefficients at the very beginning of the table.
• The syntax for the python source command has changed slightly to be more consistent with the other features of the command.
• The commands reset_atom_ids and reset_mol_ids have been renamed to reset_atoms id and reset_atoms mol, respectively. When the original commands are used, a warning is printed and the commands changed to the new versions.
• The box command has been removed. The error check that it was used for to disable has been changed to a warning. If the box command is used, it is ignored and a warning is printed.
• Binary restarts written with KOKKOS enabled for older versions of LAMMPS may not read back correctly with this version due an inconsistency in the restart output. Those restarts must be converted into data files using the old executable to be readable.

This is an update to the 23 June 2022 stable release that fixes a few bugs that have been reported since then and updates some libraries, dependencies, and build system support. There is no new functionality added.

The following individual fixes and changes are included:

• restore consistent handling of dump output frequency
• backport corrections to the DIELECTRIC package
• update/correct documentation for building the ELECTRODE package with the traditional make procedure
• avoid race condition when downloading potential files in CMake
• adapt VTK support in CMake to be compatible with VTK 9.0 and later
• correct/improve OpenMP detection for CMake 3.10+
• relax minimum required OpenMP version for KOKKOS package (based on improved OpenMP detection)
• prefer versioned cythonize command over unversioned if it matches the selected python version
• update default downloaded plumed library version to 2.8.1
• adjustments for correct HTML output of the manual with sphinx 5.1+
• add workaround for activate inactive hyperlinks for Fortran functions in manual
• correctly report mixing for CLASS2 pair styles
• increase buffer for internal regex function to accommodate larger strings
• correctly apply offsets to shake types in molecule files
• correct outdated neighborlist issues when calling delete_atoms or create_bonds multiple times
• fix buffer allocation issue for atom style dumps
• avoid segmentation faults when using the clear command with atomfile variables and pair/only package flags
• update broken URLs in the manual
• add support to detect Windows 10 22H2 in OS version info

Changes since the 15 September 2022 patch release:

• New ML-IAP package unified python interface (Steven Anaya and Nicholas Lubbers, LANL) PR #3458
• Partial Kokkos support for the ML-IAP package, (Matt Bettencourt and Markus Hrywniak, NVIDIA) PR #3487
• New pair style ylz (Mehdi Baghaee,SUSTech Shenzhen) PR #3491
• Updates and fixes to the BPM package (Joel Clemmer, SNL) PR #3448
• Updates to the ML-PACE package introducing extrapolation grade / active learning (Yury Lysogorskiy, Ruhr-Uni Bochum) PR #3315, PR #3479, PR #3490, PR #3501
• Updates and corrections to the SPIN package (Julien Tranchida, CEA) RP #3461
• Updates to the Fortran module (Karl Hammond, U Missouri) PR #3396, PR #3470, PR #3508
• Update bundled Kokkos library to version 3.7.0 (Stan Moore, SNL and the Kokkos developers) PR #3474
• Performance improvements/consistency for the KOKKOS versions of SNAP and Tersoff (Evan Weinberg, NVIDIA) PR #3465, PR #3488
• GPU package initialization improvements (Mike Brown, Intel) PR #3478
• Support for quartic interaction in pair style list (Tiedong Sun) PR #3473
• Support requesting a full neighbor list with pair style zero (Drew Rohskopf, SNL) PR #3471
• Integrate Peridynamics user guide PDF as Howto into the LAMMPS manual (Axel Kohlmeyer, Temple U) PR #3462
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3450, PR #3454, PR #3455, PR #3456, PR #3459, PR #3463, PR #3468, PR #3475, PR #3477, PR #3480, PR #3482, PR #3485, PR #3489, PR #3495, PR #3497, PR #3498, PR #3500, PR #3502, PR #3503, PR #3504, PR #3507, PR #3510

Backward compatibility notes:

• the default setting for neighbor list rebuilds has been changed from delay 10 to delay 0 to guarantee correctness at some modest performance loss. This can lead to more frequent neighbor list rebuilds or neighbor list rebuilds on different timesteps and thus diverging trajectories.
• Unlike other variables, atomfile style variables are now deleted with the clear command. This avoids segmentation faults due to trying to access a deleted fix store/peratom instance.

Changes since the 3 August 2022 patch release:

• Add basic support for symbolic types aka type labels (Jake Gissinger, NASA, Yaser Afshar, UMN, Steve Plimpton, SNL, Axel Kohlmeyer, Temple U) PR #2531
• New fix pair command to access per-atom quantities computed by pair styles, also dump_modify skip option to skip writing dump frames depending on a condition (Steve Plimpton, SNL) PR #3369
• Major update of the mesocnt pair style with addition of mesocnt bond and angle styles and more to complete the functionality (Philipp Kloza, U Cambridge) PR #3421
• Updates and corrections for plugin handling in LAMMPS and the MDI package (Christian Negre, LANL, and Taylor Barnes, MOLSSI, and Steve Plimpton, SNL) PR #3366
• Add support for using fix shake and fix rattle during minimization by replacing the constraints with strong restraints (Axel Kohlmeyer, Temple U) PR #3244
• Remove some bias from the operation of fix bond/swap caused by how LAMMPS stores neighbors and bonds (Steve Plimpton, SNL) PR #3444
• Add support to fix latte so it can be used in combination with fix gcmc and similar (Steve Plimpton, SNL) PR #3436
• Split internal fix STORE command into fix STORE/GLOBAL and fix STORE/PERATOM (Axel Kohlmeyer, Temple U) PR #3379
• Update embedded fmtlib code to version 9.1.0 (Axel Kohlmeyer, Temple U) PR #3381, PR #3418
• Tune INTEL package code for better performance with the new LLVM based Intel compiler (Michael Brown, Intel) PR #3410
• Various contributions from participants at the LAMMPS Code Clinic event (multiple authors).
  • Project 1: Improved error messages: PR #3394, PR #3403, PR #3408, PR #3428
  • Project 2: Refactor for new APIs: PR #3391, PR #3398, PR #3399, PR #3401
  • Project 4: Modernize documentation: PR #3411, PR #3427
  • Project 5: Add expand and new tests: PR #3400, PR #3407, PR #3438
• Many small bug fixes, minor code improvements and refactoring, and coding style, build system, documentation, formatting updates (multiple authors) PR #3378, PR #3380, PR #3382, PR #3383, PR #3384, PR #3387, PR #3388, PR #3389, PR #3390, PR #3392, PR #3393, PR #3395, PR #3406, PR #3409, PR #3414, PR #3419, PR #3420, PR #3422, PR #3425, PR #3432, PR #3433, PR #3440, PR #3442 , PR #3443

Compatibility with external tools:

• TopoTools in VMD must be at least version 1.9 to be compatible with type labels. To update your VMD TopoTools plugin, you can download it from the TopoTools release page on GitHub
• OVITO is going to be compatible with data files containing type labels soon

Backward compatibility notes:

• external LAMMPS code that uses fix STORE will need to be updated
• the update of the mesocnt styles is not backward compatible
• comments in data and data files must have a blank between the last valid input and the comment character '#'
• the mandatory fourth argument (NULL) for fix latte is no longer required. Its function is moved to the coulomb keyword

This is an update to the 23 June 2022 stable release that fixes a few bugs that have been reported since then and updates some libraries, dependencies and the CMake support for plugins on Windows.

The following individual changes are included:
The following individual fixes and changes are included:

• Fix corner case with if-then-else Boolean logic where there is just a single string argument.
• Also remove references to comparing strings with Boolean operaters like "<" or ">=" in the documentation.
• Add missing atom->grow() to Kokkos unpack_exchange to avoid segmentation fault
• Fix small memory leak in ML-SNAP
• Avoid possible out-of-bounds data access in ML-RANN
• Bugfixes to fix bond/react
• Bugfixes to pair style mgpt
• Avoid segfault in dump vtk when used without a region
• Allow ramp(x,y) variable function to be used in between runs (returning x) and avoid division by zero when used with run 0.
• Allow vdisplace(), swiggle(), and cwiggle() functions to be used in between runs and disallow using them with fix dt/reset.
• Prevent view bounds error when building the Kokkos neigh list and a proc has no atoms
• Add missing GPU <--> CPU data transfer in Kokkos minimize, gave wrong results when using comm no or comm/reverse no running on the GPU
• fixes for CMake scripts used for building plugins to cross-compile with MPI on Windows
• CMake scripting updates to fix multiple issues building the n2p2 library on Ubuntu 18.04LTS and 20.04LTS
• add CMake script code to provide a "make package" target when cross-compiling plugins to Windows
• mention dump style cfg/uef in the main dump manual page
• add missing support for dump_modify colname to local dumps
• add more unit tests to improve test coverage of boolean evaluations
• must not search for MPI package when MPI is disabled to avoid issues with testing the LAMMPS Fortran module
• update embedded Kokkos library to bugfix release version 3.6.1
• update googletest library from a snapshot to release version 1.12.1
• update the Viscosity howto input script example to simulate liquid argon as advertised
• avoid deprecation warnings when building the manual
• update python package version requirements for building the manual