Public development project of the LAMMPS MD software package
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Published by akohlmey over 3 years ago
Changes since the 14 May 2021 patch release:
rann
and matching potential files for using "rapid atomistic neural network (RANN) potentials (Christopher Barrett and Doyl Dickel, Mississippi State) PR #2570www.lammps.org
and docs.lammps.org
instead of lammps.sandia.gov
and add tool to check for it and convert such links, also corresponding updates to the LAMMPS manual itself. (Axel Kohlmeyer and Richard Berger, Temple U) PR #2778, PR #2768Backward compatibility notes:
https://lammps.sandia.gov
to https://www.lammps.org
(please report cases where links need to be updated).Published by akohlmey over 3 years ago
Changes since the patch release 8 April 2021:
pace
computing interactions using the Atomic Clusterhybrid/scaled
that allows combining contributions from different pair styles with constant or variable scaling factors (Axel Kohlmeyer, Temple U) PR #2702Command
that all command styles are now derived from instead of the Pointers
class (Axel Kohlmeyer, Temple U) PR #2707spin
in the KOKKOS package (Julien Tranchida, Stan Moore, and Svetoslav Nikolov, SNL) PR #2693Backward compatibility notes:
comm_modify multi
now requires to also use neighbor multi
. In case the new neighbor multi
functionality causes problems, it is possible to revert to the previous implementation with neighbor multi/old
. In that case comm_modify multi/old
and comm_modify cutoff/multi/old
need to be used for enabling and customizing multi-cutoff ghost atom communication.Published by akohlmey over 3 years ago
Changes since the patch release 10 March 2021:
Backward compatibility notes:
Published by akohlmey over 3 years ago
Changes since the patch release 10 February 2021:
kim_<something>
commands there is now only the kim
command which accepts <something>
as subcommand. Additional cleanups and improvements to the kim commands (Yaser Afshar, Ryan S. Elliott, Ellad Tadmor UMN) PR #2620, PR #2625, PR #2649Backward compatibility notes:
kim_<command>
are renamed to kim <command>
Published by akohlmey over 3 years ago
Changes since the patch release 24 December 2020:
math_vector.h
with calls to MathExtra
namespace functions. Obsolete math_vector.h
and math_complex.h
header files that were using common c++ class names without a protecting namespace (Axel Kohlmeyer, Temple U) PR #2558Backward compatibility notice:
fix_modify energy
and fix_modify virial
has been changed. It is now only available for fixes that contribute to the potential energy and the virial. The energy contributions from thermostats and similar fixes can be accessed with the thermo keyword ecouple
and the conserved quantity (i.e. etotal + ecouple) is available as econserve
. There are corresponding changes to the implementation, so external fixes will have to be adapted or they will no longer compile. All affected fixes in the LAMMPS distribution have been updated.__version__
module variable and upon initialization of a LAMMPS instance it is checked against the output from the lammps.version()
method which returns the version of the loaded shared library. If they don't match an exception is raised. This helps to detect inconsistent installations of the shared library or module or incorrectly setting LD_LIBRARY_PATH
or PYTHONPATH
.c_ID
, f_ID
, v_ID
with and without indices) are now more strictly checked for correctness. Inputs that are incorrect but have previously worked by chance will now cause failures.Published by akohlmey almost 4 years ago
Changes since the patch release 30 November 2020:
Backward compatibility notice:
Published by rbberger almost 4 years ago
Changes since the patch release 29 October 2020:
gaussian
, E. Voyiatzis (Royal DSM), PR #2440shake
and forward comm on Device for fixes, Stan Moore (SNL), PR #2441spin/exchange/biquadratic
, Julien Tranchida (SNL), PR #2410molecule
keyword to bond react
to optionally force reaction to be inter- or intramolecular, Jacob Gissinger (NASA), PR #2467lammps_gather_atoms
, Richard Berger (Temple U), PR #2466libyaml
in case it is not found locally, Axel Kohlmeyer (Temple U), PR #2476fmtlib
to version 7.1.3, Axel Kohlmeyer (Temple U), PR #2451, PR #2487sublo
, subhi
, sublo_lambda
, and subhi_lambda
globals, Richard Berger (Temple U), Axel Kohlmeyer (Temple U), PR #2420universe_size
, universe_rank
, world_size
, and world_rank
settings, Axel Kohlmeyer (Temple U) PR #2420newton_bond
and newton_pair
settings, Axel Kohlmeyer (Temple U), PR #2487-in none
argument so that multi-partition runs can be launched from the library interface without an (initial or dummy) input file, Axel Kohlmeyer (Temple U), PR #2420read_data
, Axel Kohlmeyer (Temple U), Steve Plimpton (SNL), PR #2419react
, Jacob Gissinger (NASA), PR #2467pair spin/exchange
interactions, older restart files will no longer be compatibleneighbor/history
data.bond/react
: updates map file section title from 'BondingIDs' to 'InitiatorIDs'. Old section title still works for backward compatibility, with a printed warning that it has been deprecatedPublished by akohlmey almost 4 years ago
This stable release corresponds to a significantly larger number of changes than between previous stable releases. There have been over 4000 commits added since the last stable release, while the two previous stable releases have been made after fewer than 2000 commits.
strtok()
function. This has lead to substantial reduction in the lines of code used for those cases.utils
namespace. Several new additions of such convenience functionsconst std::string &
instead char *
or const char *
as function argument in many places to simplify string processing and replacing C style string functions with their equivalent or expanded functionality of std::string
member functionsprintf()
style functions since no special treatment is required for processing bigint or tagint arguments. Since fmtlib has been accepted as a C++20 feature, this is also future proofing the code base.NULL
with nullptr
where applicable for better detection of incorrect use.ctest
tool that comes with CMake. Tests for a variety of features and styles are included with a code coverage close to 40%. The added tests have exposed a significant number of previously unknown bugs and inconsistencies (e.g. between plain pair styles and suffixed versions or between Pair::compute()
and Pair::single()
) in the code base, which have been fixed.#include ""
statements has been revised and the lists updated where possible after analyzing with the IWYU tool.reset_mol_ids
fix widom
for modeling Widom insertionsfix pafi
to perform langevin or brownian dynamics time integration constrained to a potential hyperplane. Intended to be coupled to the PAFI C++ code.fix bond/react
in particular RMSD based constraints.fix accelerate/cos
and compute viscosity/cos
in USER-MISC as yet another method to compute viscosity.fix momentum/chunk
to remove per chunk momentumspecial
to provide a mechanism to implement special bond exclusions beyond 1-4.binary2atom
tool to become consistent with current text mode custom dumpsexamples/COUPLE/fortran
and examples/COUPLE/fortran2
wrappers to become compatible with updates to the C-library interface. Also work on a new, "object oriented" Fortran interface has started.reset_ids
was renamed to reset_atom_ids
.Published by akohlmey almost 4 years ago
These are the final changes for the stable release.
Changes since the patch release 22 October 2020:
Published by akohlmey almost 4 years ago
This is the second release candidate for a new stable release. Please test thoroughly and give feedback, so we can address bugs and issues in the stable release. We are particularly interested in issues with compiling LAMMPS on all kinds of platforms beyond what we usually test on.
Changes since the patch release 9 October 2020:
dpd/tstat/gpu
and dpd/gpu
so they can be used together with a hybrid pair style (Trung Nguyen, Northwestern U) PR #2402Published by akohlmey about 4 years ago
This is the first release candidate for a new stable release. Please test thoroughly and give feedback, so we can address bugs and issues in the stable release. Since the last stable release the code base has seen some significant modernization and refactoring and also the documentation has been updated and partially reorganized to include more information aimed at developers either writing applications that use LAMMPS as a library or that are working on extending LAMMPS. Because of that we are particularly interested in problems with building LAMMPS on different platforms and formatting issues of the new parts of the manual, or problems building it. Matching singularity container images with tested toolchains have been uploaded to the Singularity container library.
Changes since the patch release 18 September 2020:
Backward compatibility note:
lammps_open()
now need to define LAMMPS_LIB_MPI, so that library.h can also be used in cases where there is no MPI library installed. Also it should be noted, that calling lammps_open_no_mpi()
is equivalent to calling lammps_open()
with MPI_COMM_WORLD, so lammps_open()
is really only needed when running LAMMPS on a subset of the MPI ranks with a custom communicator created by MPI_Comm_split()
as demonstrated in examples/COUPLE/simple/simple.c
Published by akohlmey about 4 years ago
This is the last patch release with new features before we will prepare for a stable release due in 2-3 weeks. Please test thoroughly and give feedback, so we can address bugs and issues in the stable release. The code base has seen some significant modernization and refactoring and also the documentation has been updated to include more information aimed at developers either writing applications that use LAMMPS as a library or that are working on extending LAMMPS.
Changes since the patch release 24 August 2020:
NULL
with the C++11 nullptr
keyword, where meaningful. (E. Anne Gunn, Sheridan College) PR #2358make iwyu
target to run the include-what-you-use tool (Axel Kohlmeyer, Temple U) PR #2338Backward compatibility notice:
void **
argument to lammps_open()
and similar functions is deprecated and the void *
return value should be used instead. Also it implements some symbolic constants that should replace the explicit numbers from previous revisions of the API (the values are unchanged).Published by akohlmey about 4 years ago
This is a minor update to patch release 21 August 2020. It contains only bugfixes and updates to the documentation:
Published by akohlmey about 4 years ago
Changes since the patch release 21 July 2020:
{fmtlib}
to version 7.0.2, also change its internal ABI to avoid clashes with other uses of that library (Richard Berger, Temple U), PR #2276tools/phonon
with current release from its github repo (Ling-Ti Kong, Shanghai Jiao Tong U) PR #2258tiled
communication style to make it work with triclinic cells including load balancing support and support for multi-cutoff communication and the PPPM KSpace styles (Adrian Diaz, U Florida and Steve Plimpton, SNL) PR #1296, PR #1426, PR #2259, PR #2280Backward compatibility notice:
Published by akohlmey about 4 years ago
Changes since the patch release 30 June 2020:
reset_mol_ids
that will reassign molecule IDs based on topology data. This can be applied to the entire system or a subset. (Steve Plimpton SNL, Jake Gissinger U Colorado, Axel Kohlmeyer Temple U) PR #2218Backward compatibility notices:
reset_ids
command has been renamed to reset_atom_ids
compute fragment/atom
have been changed due to significant performance optimizations. Please review the documentation for details.Published by akohlmey over 4 years ago
Changes since the patch release 15 June 2020:
UNITS:
tag. This extends the functionality of PR #2159 (Axel Kohlmeyer, Temple U) PR #2183, PR #2198Modify::add_fix()
and Modify::add_compute()
that allows creating a fix from a single string instead of having to provide a list of strings and the length of that list. (Axel Kohlmeyer, Temple U) PR #2191, PR #2199, support for Group::assign
(Jake Gissinger, CU Boulder) PR #2195std::string
and convenience functions in the utils namespace (Axel Kohlmeyer, Temple U) PR #2190, PR #2201Backward compatibility notices:
create_atoms
was incorrectly using radians instead of degrees (as stated in the documentation) due to a missing conversion. This patch implements the conversion from degrees to radians and thus all previous inputs using this option will produce different results.Published by akohlmey over 4 years ago
Please note that this release contains several important bugfixes for recent refactoring changes included in the 2 June 2020 version. The 2 June 2020 version should not be used anymore and replaced with this version.
Changes since the patch release 2 June 2020:
tubular potential model
(TPM). This consist of a Fortran library, a pair_style and compute, and tools for generating force field files. Pair style mesocnt
, which implements the same model in C++-only has been moved from USER-MISC to this package (Maxim V. Shugaev & Leonid V. Zhigilei, University of Virginia, Alexey N. Volkov, University of Alabama) PR #1873pair_write
and bond_write
will add these as the first line when a file is newly created and all subsequent attempts to append a table will check for consistent units or error out (Axel Kohlmeyer, Temple U) #2159reset_ids
command to obtain consistent atom ids in parallel regardless of the number of MPI ranks (Steve Plimpton, SNL) PR #2142union ubuf
definitions in lmptype.h header file instead of individual classes (Axel Kohlmeyer, Temple U) PR #2151Backward compatibility notices:
mesocnt
pair style now need to install the USER-MESONT package instead of USER-MISCPublished by akohlmey over 4 years ago
Changes since the patch release 5 May 2020:
utils::logmesg()
convenience function to send string to both, screen and logfile, with one call. Axel Kohlmeyer (Temple U), PR #2103Backward compatibility notices:
Published by akohlmey over 4 years ago
Changes since the patch release 15 April 2020:
fix accelerate/cos
and compute viscosity/cos
in USER-MISC as yet another method to compute viscosity (Zheng Gong, École normale supérieure de Lyon) PR #2019Backward compatibility notices:
Published by akohlmey over 4 years ago
Changes since the patch release 19 March 2020:
kim_property
command in the KIM package (Yaser Afshar, Ellad Tadmor, Daniel S. Karls, Ryan Elliott , UMN) PR #1946Backward compatibility notice:
mode=static
(the default) and mode=shared
. The previous choices are still available and mapped to one of them (i.e. mode=exe
and mode=lib
will set mode=static
, and mode=shexe
and mode=shlib
will set mode=shared
).