LAMMPS Files

This is the fifth update to the 22 July 2025 stable release that fixes bugs that have been reported since the fourth update and backported from the development version.

The following individual changes are included:

• backport of [24aadf]
• backport memory fixes from PR [#5108]
• backport fix wall/gran bugfix from PR [#5007]
• correct embedding rpath into LAMMPS executable in macOS app bundles
• fix spurious "chunks do not contain all atoms in molecule" warning in compute chunk/atom
• disallow unions or intersections or regions that may translate or rotate since those are broken (pending fix to force consistent motion is in upstream)
• correct torque application in pair style tri/lj
• disambiguate non-virtual overloads in KOKKOS support for REAXFF so that clang is happy without segfaults
• avoid segfault in fix shake/kk destructor because of using incorrect/stale copy of nlocal
• fix memory leak when deleting vector style variables
• do not ignore comment lines for fix ttm/mod input
• fix wrong argument index in pair oxdna/stk potential file reader
• initialize remap plan pointers to nullptr after allocation
• fix dump vtk parallel summary referencing wrong piece files
• reject region-restricted translations in fix gcmc that cannot be placed
• speed up region-restricted gas-atom list rebuild
• fix potential crash in pair style peri/eps due insufficient allocation of theta array
• fix pair brownian/poly Newton's 3rd law violation for random forces
• Disable use of volume fraction correction for brownian/poly
• fix per-type-pair bond-breaking criterion in PERI package pair styles
• make sure torque arrays are initialized to zero before use in lj/log/dipole/long
• backported GPU library fixes for issues detected on AMD 780M APU from [#5015]
• fix issue in MLIAP unified
• allocate bonded coefficient views in allocate() instead of coeff() for KOKKOS styles
• REACTION: fix segfault when reading fix bond/react per-atom properties from a data file
• KOKKOS: evaluate the pair reaxff/kk bond-order exponentials in double precision to avoid overflow
• KOKKOS: avoid floating-point exceptions in 16 bond, dihedral and improper styles (trips FPE-trapping builds)
• core: improve error messages when a variable references a mismatched compute or fix property
• REPLICA: call kspace->setup() from fix pimd/langevin when the volume changes
• RIGID: support more than 2 billion bodies in fix rigid/small (issue [#4038])
• KOKKOS: add the missing fence after pack_reverse_self in reverse_comm_device (race condition)
• core: avoid integer overflow in compute temp/sphere for large systems
• KOKKOS: correct the order of the conditionals in remap_kokkos
• MC: reproduce the fix gcmc random number sequence exactly after a restart
• COLVARS: update size_vector when fix_modify changes the number of colvars
• core: fix infinite loop in compute_modify and let computes see and override extra/dof and dynamic/dof
• core: avoid a segfault when printing the error indicator line for a missing command argument
• MACHDYN: use double instead of float in pair smd/triangulated/surface and remove debug code
• SPIN: fix hang of fix nve/spin in parallel when a sector contains atoms outside the fix group
• core: reject fix adapt diameters that would give zero mass or a negative diameter
• build: define FFT_KOKKOS_FFTW_THREADS in CMake so KOKKOS FFT threading is actually enabled
• MOLECULE: add the missing copymode guard to the bond style base destructors (double free)
• ASPHERE: avoid excessive torque in pair gayberne when the determinant is very small
• GRANULAR: fix kinetic energy gain of fix wall/gran hooke/history for grazing frictional impacts (the corresponding doc update is already on maintenance)
• EXTRA-FIX: warn when fix ttm/mod is used with a restricted coupling region; correct the Si example
• DPD-REACT: grow duCond/duMech with nmax instead of recreating them every step
• DPD-REACT: remove per-step malloc/free in pair exp6/rx, pair multi/lucy/rx and pair mesocnt
• KOKKOS: stop fix acks2/reaxff/kk from silently producing wrong results with a reduced precision KOKKOS library
• REPLICA: validate the swap partner index in fix temper, fix temper/npt and fix temper/grem
• RIGID: initialize molecule[] for atoms outside the group and fix the file handling in readfile()
• ML-IAP: use SafeFilePtr in MLIAPModelSimple::read_coeffs, which reused a closed file handle and leaked it on errors
• core: guard Replicate::newtag against topology data referencing a non-existent atom
• PHONON: initialize and check the pivot indices in FixPhonon::GaussJordan
• KSPACE: fix the slab correction self-energy of ewald/dipole, ewald/dipole/spin and pppm/dipole/spin
• KOKKOS: fix the flipped forward/backward flag in fft_3d_1d_only_kokkos
• COUPLE: plug a memory leak on failed plugin loads in the plugin loader
• SPIN: call the collective error function on all ranks in pair_style spin so parallel runs abort instead of hanging
• SPIN: apply the Zeeman field unit conversion in fix precession/spin only once
• SPIN: initialize the symmetric cutoff pairs in pair spin/neel
• core: fix the column selection for 2d single-value averaging in fix ave/grid
• AMOEBA: fix the corrupted sorting of the 1-3 neighbor list in kmpole()
• OPENMP: fix per-atom energy indexing in the TIP4P /omp pair styles
• DPD-MESO: do not tally heat flux from stale data for neighbors beyond the temperature cutoff in pair edpd
• DPD-MESO: clamp the correct random number for the eDPD random heat flux
• EXTRA-FIX: use current unwrapped coordinates and the correct energy index in fix efield/tip4p
• ASPHERE: do not tally stale sub-particle force data in pair line/lj and pair tri/lj
• RIGID: restrict momentum resampling in fix rigid/small to bodies inside the fix group
• MOFFF: avoid multiplying with an uninitialized inverse distance in angle cosine/buck6d
• core: fix three copy-paste errors in the parsing of the region cone hi boundary
• core: return a valid contact point for rim contacts with an open side face of region cylinder
• EXTRA-COMPUTE: do not read past the number of neighbors in compute ackland/atom
• MC: store all global settings of pair dsmc in the restart file
• PHONON: honor the documented default output file of dynamical_matrix and third_order
• MISC, ML-RANN: harden the potential file parsing of pair agni and pair rann
• core: fix destructor safety on error paths and missing size checks in MyPoolChunk, fix halt, fix vector and fix imd
• KOKKOS: fix the memory usage reporting and uninitialized members of fix reaxff/bonds/kk
• core, RIGID, MANYBODY: handle fully open region block/prism, garbage accumulator indices in pair bop, and uninitialized rigid body bonus pointers
• MANYBODY: avoid an out-of-bounds read in single() of pair local/density
• PHONON: plug two memory leaks and guard against calling ferror() on a null file pointer in third_order
• KSPACE: accumulate the slab correction into the reported energy in pppm/tip4p and pppm/tip4p/omp
• KSPACE: evaluate all TIP4P slab correction terms at the virtual charge site
• core: do not leak memory in 10 fixes and computes when the same argument is given more than once
• KSPACE: fix uninitialized data, grid communication buffer sizes and per-atom energy/virial in pppm/dipole/spin
• SPH, GPU: accumulate the long-range correction of pair sph/lj outside the neighbor list loop
• DPD-SMOOTH: make the random number seeding of pair sdpd/taitwater/isothermal independent of the command order
• EXTRA-FIX: set the missing extscalar flag in fix ffl
• EXTRA-FIX: initialize the r-RESPA level count in fix electron/stopping/fit
• GPU: fix a GPU memory fault in pair edpd/gpu when no power/kappa tables are used
• FEP, INTERLAYER: match hybrid pair styles by prefix so an active suffix does not break the sub-style checks
• COLVARS: correct the wrap function of orientation_angle (upstream Colvars PR 943)
• MISC: do not request the accelerated fix NEIGH_HISTORY from pair tracker, which does not support it
• RIGID, SRD: fix the rigid body update for line and triangle particles
• RIGID: fix the rotation of line particles inside rigid bodies
• REPLICA: reset max_nlocal in fix pimd/nvt so that buf_beads[i] is reallocated
• MANYBODY: count funcfl data in pair eam only after the file was read successfully
• core: make Input::execute_command exception safe so failed commands do not leak
• KSPACE: make the kspace_modify mix/disp setting work for ewald/disp
• KOKKOS: discard the stale small system neigh/thread heuristic in the package kokkos command
• core: return no contact from regions with all faces open instead of unassigned coordinates
• GRANULAR: get the neighbor history fix of fix granular/mdr from the pair style instead of a hardcoded ID
• BOCS, EXTRA-FIX: initialize members read before first use in compute pressure/bocs and fix controller
• REAXFF: correct the member names used to initialize the fix qeq/reaxff sparse matrix
• KOKKOS: fix six correctness defects in mliap/so3/kk, compute temp/deform/kk, pair exp6/rx/kk, fix wall/gran/old and fix wall/region/kk
• ML-IAP: avoid an integer overflow before the intended 64-bit atom count handling
• DPD-REACT, KOKKOS: add the missing rx mixing weight sanity checks and release Kokkos views promptly
• core: do not reject zero-size global fix state when reading a restart file (granular history and BPM restarts)
• GRANULAR: do not request the accelerated fix NEIGH_HISTORY from pair granular, which does not support it
• core: error out instead of crashing on invalid variable references in next, py_ functions, fix store/state and fix ave/grid
• GRANULAR, MDI: consistent MDR wall guard, leak on repeated mdi plugin keywords, uninitialized history pointers in pair granular single()
• several: validate user parameters used as divisors or lookups in pair exp6/rx, fix adapt, pair meam, fix rheo, fix pour and pair gauss
• MANYBODY: delete the allocated temporary storage when reading an EAM potential file fails
• REACTION, PHONON, tools: check createIDs in fix bond/react, plug the largest leak in third_order, avoid passing NULL to fread in binary2txt
• several: input validation for restart files and -reorder, SMTBQ tail coefficients, failed dynamic_cast in fix granular/mdr, keyword leak in fix reaxff/species
• MISC, ML-SNAP, DIPOLE: validate the fix imd message length, require positive widths in compute gaussian/grid/local, initialize muj in pair lj/long/dipole/long
• many: assorted defensive hardening across a dozen styles from the Coverity scan triage
• core and several packages: range checks on counts and string lengths read from binary restart files and fix bond/react map files
• Avoid a segfault in finish.cpp when a NEB calculation would skip the initial regular NEB run.

Full Changelog: https://github.com/lammps/lammps/compare/stable_22Jul2025_update4...stable_22Jul2025_update5

Information on the files attached to this release:

• lammps-src-22Jul2025_update5.tar.gz - LAMMPS source code with translated manual in HTML and PDF format included
• lammps-linux-x86_64-22Jul2025_update5.tar.gz - Fully static LAMMPS binaries for all Linux machines with x86_64 CPUs
• Manual_22July2025.pdf - PDF version of full manual for LAMMPS

There are no binary packages containing LAMMPS and LAMMPS-GUI for this update release. Sorry.

We strongly recommend to upgrade to LAMMPS-GUI version 3.1 instead, which is not compatible with this LAMMPS version and will be released alongside the next LAMMPS stable release. You can download the latest LAMMPS-GUI releases from https://github.com/akohlmey/lammps-gui/releases. LAMMPS-GUI has seen significant updates and improvements in the last 12 months since it was split form the LAMMPS distribution and moved to a git repository of its own. Many of those improvements depend on changes in the LAMMPS code. Of course, you are free to compile the legacy version of LAMMPS-GUI on your own from the source code in the tools/lammps-gui folder.