[pull] develop from lammps:develop

cmake/packaging/org.lammps.lammps-gui.yml

@@ -84,7 +84,6 @@ modules:
       - -D PKG_ML-IAP=yes
       - -D PKG_ML-PACE=yes
       - -D PKG_ML-POD=yes
-      - -D PKG_ML-RANN=yes
       - -D PKG_ML-SNAP=yes
       - -D PKG_ML-UF3=yes
       - -D PKG_MOFFF=yes

cmake/presets/all_off.cmake

@@ -61,7 +61,6 @@ set(ALL_PACKAGES
   ML-PACE
   ML-POD
   ML-QUIP
-  ML-RANN
   ML-SNAP
   ML-UF3
   ML-RUNNER

cmake/presets/all_on.cmake

@@ -63,7 +63,6 @@ set(ALL_PACKAGES
   ML-PACE
   ML-POD
   ML-QUIP
-  ML-RANN
   ML-SNAP
   ML-UF3
   ML-RUNNER

cmake/presets/mingw-cross.cmake

@@ -48,7 +48,6 @@ set(WIN_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-POD
-  ML-RANN
   ML-SNAP
   ML-UF3
   MOFFF

doc/src/Commands_bond.rst

@@ -22,9 +22,11 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT.
    *
    *
    *
+   * :doc:`bpm/peri <bond_bpm_peri>`
    * :doc:`bpm/rotational <bond_bpm_rotational>`
    * :doc:`bpm/spring <bond_bpm_spring>`
    * :doc:`bpm/spring/plastic <bond_bpm_spring_plastic>`
+   * :doc:`bpm/zero <bond_bpm_zero>`
    * :doc:`class2 (ko) <bond_class2>`
    * :doc:`fene (iko) <bond_fene>`
    * :doc:`fene/expand (ko) <bond_fene_expand>`

doc/src/Commands_pair.rst

@@ -23,7 +23,6 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT.
    *
    *
    * :doc:`adp (ko) <pair_adp>`
-   * :doc:`agni (o) <pair_agni>`
    * :doc:`aip/water/2dm (t) <pair_aip_water_2dm>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/bc (o) <pair_airebo>`
@@ -46,6 +45,7 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT.
    * :doc:`born/coul/wolf (gko) <pair_born>`
    * :doc:`born/coul/wolf/cs (go) <pair_cs>`
    * :doc:`born/gauss (ko) <pair_born_gauss>`
+   * :doc:`bpm/peri <pair_bpm_peri>`
    * :doc:`bpm/spring <pair_bpm_spring>`
    * :doc:`brownian (ko) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
@@ -270,7 +270,6 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t = OPT.
    * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
-   * :doc:`rann <pair_rann>`
    * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`rebomos (o) <pair_rebomos>`

doc/src/Commands_removed.rst

@@ -17,6 +17,33 @@ stop LAMMPS and print a suitable error message in most cases, when a
 style/command is used that has been removed or will replace the command
 with the direct alternative (if available) and print a warning.
 
+ML-RANN package
+---------------
+
+.. deprecated:: TBD
+
+.. index:: pair_style rann
+
+The ML-RANN package and its pair style *rann* have been removed because
+they were unmaintained in LAMMPS for a long time and caused to much work
+to keep it aligned with the LAMMPS coding conventions.  The ML-RANN
+developers are maintaining an independent fork of their code.  They plan
+to submit a second generation of their package when it is ready.  Until
+then we recommend to use the LAMMPS 22Jul2025 stable version if you want
+to use this package.
+
+Pair style agni
+---------------
+
+.. deprecated:: TBD
+
+.. index:: pair_style agni
+.. index:: pair_style agni/omp
+
+The pair style *agni* has been removed since it was unmaintained
+for a long time and its developers have moved on to alternate
+machine learning potentials that are more efficient and accurate.
+
 amber2lmp tools
 ---------------
 
@@ -34,6 +61,10 @@ ATC, AWPMD, and POEMS packages
 
 .. deprecated:: 10Sep2025
 
+.. index:: fix poems
+.. index:: fix atc
+.. index:: pair_style awpmd/cut
+
 The ATC, AWPMD, and POEMS packages are removed because they were
 unmaintained for a long time and their legacy C++ programming style
 started to create problems with modern C++ compilers.  LAMMPS version 22
@@ -126,6 +157,8 @@ MSCG package
 
 .. deprecated:: 21Nov2023
 
+.. index:: fix mscg
+
 The MSCG package has been removed from LAMMPS since it was unmaintained
 for many years and instead superseded by the `OpenMSCG software
 <https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
@@ -136,6 +169,8 @@ LATTE package
 
 .. deprecated:: 15Jun2023
 
+.. index:: fix latte
+
 The LATTE package with the fix latte command was removed from LAMMPS.
 This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
 and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package

doc/src/Howto_granular_surfaces.rst

@@ -97,6 +97,40 @@ or Lines section, then triangles/lines will be read in and distributed
 along with any particles the data file includes, assuming an appropriate
 :doc:`atom_style <atom_style>` has been specified, as explained below.
 
+.. image:: img/mixer-drum.jpg
+   :width: 50%
+
+.. admonition:: Re-using STL files for 3d-printing
+
+   There are a large number of STL files published and available for
+   download that were generated for 3d-printing (see the cement mixer
+   drum above for example, that was created for printing a cement truck
+   toy model).  Those can in principle be used with LAMMPS, but there
+   are a couple of quirks to watch out for.  Those STL files may contain
+   degenerate triangles; this is not a problem for 3d-printing but for
+   LAMMPS.  LAMMPS will either try to ignore those triangles or stop
+   with an error.  Another issue are duplicate triangles.  Those will
+   double the force in LAMMPS which is not likely what you want.
+   Finally, those STL files may have very long and narrow triangles.
+   These force LAMMPS to have a very large neighbor list and a long
+   communication cutoff (both are detected and warnings or errors are
+   printed).
+
+   Thus in many cases, it is advisable to *remesh* the STL file, i.e.
+   recreate the surface(s) with more regular and fewer triangles.  One
+   option to do this is by using `MeshLab or PyMeshLab
+   <https://meshlab.net>`_.  Here is an example:
+
+   .. code-block:: Python
+
+      import pymeshlab
+      ms = pymeshlab.MeshSet()
+      ms.load_new_mesh('input.stl')
+      ms.meshing_isotropic_explicit_remeshing(iterations=5,
+        targetlen=pymeshlab.PercentageValue(1.0)  # target edge length as % of bbox diagonal
+      )
+      ms.save_current_mesh("output.stl")
+
 ----------
 
 Surface attributes

doc/src/Howto_peri.rst

@@ -1,9 +1,18 @@
 Peridynamics with LAMMPS
 ========================
 
-This Howto is based on the Sandia report 2010-5549 by Michael L. Parks,
-Pablo Seleson, Steven J. Plimpton, Richard B. Lehoucq, and
-Stewart A. Silling.
+.. note::
+
+   Most of the content in this Howto document is is based on the Sandia
+   report 2010-5549 by Michael L. Parks, Pablo Seleson,
+   Steven J. Plimpton, Richard B. Lehoucq, and Stewart A. Silling.
+
+----
+
+.. contents:: Available topics
+   :local:
+
+----
 
 Overview
 """"""""
@@ -79,6 +88,138 @@ Some notes on this input example:
   :doc:`timestep <timestep>` command.
 
 
+BPM-based peridynamics
+""""""""""""""""""""""
+
+.. versionadded:: TBD
+
+The same four constitutive models are also available through the
+:doc:`bond_style bpm/peri <bond_bpm_peri>` command, which recasts
+peridynamics within the :doc:`BPM (bonded particle model) package
+<Howto_bpm>`.  Peridynamic bonds become real LAMMPS bonds, so the model
+uses the standard :doc:`atom_style bond <atom_style>` (no dedicated atom
+style) and the domains of solid bodies can be controlled using standard
+LAMMPS commands such as :doc:`create_bonds <create_bonds>` or
+:doc:`delete_bonds <delete_bonds>` or by reading bonds from a data file.
+This allows one to create distinct solid bodies within arbitrary
+distances or create small flaws within a body like a crack or void. Each
+bond stores per-bond reference state in :doc:`restart files <restart>`,
+and gains BPM tooling such as broken-bond dumps.  The constitutive law
+is the first :doc:`bond_coeff <bond_coeff>` argument (*pmb*, *lps*,
+*ves*, or *eps*), and a companion :doc:`pair_style bpm/peri
+<pair_bpm_peri>` provides the short-range contact force.
+
+Migrating inputs from the PERI package to BPM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Here is the minimal example above expressed in the BPM framework:
+
+.. code-block:: LAMMPS
+
+   units           si
+   dimension       3
+   boundary        s s s
+   atom_style      bond
+   atom_modify     map array
+   special_bonds   lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
+   newton          on off
+   neighbor        0.0010 bin
+   lattice         sc 0.0005
+   region          target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
+   create_box      1 target bond/types 1 extra/bond/per/atom 60 extra/special/per/atom 100
+   create_atoms    1 region target
+
+   # nodal mass (per-type) and nodal volume (the lone user-declared input)
+   mass            * 2.75e-7
+   fix             vol all property/atom d_vfrac d_damage ghost yes
+   set             group all d_vfrac 1.25e-10
+
+   pair_style      bpm/peri
+   pair_coeff      * * 1.6863e22 0.0015001
+   create_bonds    many all all 1 0.0 0.0015001
+   special_bonds   lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
+
+   bond_style      bpm/peri
+   bond_coeff      1 pmb 1.6863e22 0.0015001 0.0005 0.25
+   compute         dmg all property/atom d_damage
+   fix             1 all nve
+   timestep        1.0e-7
+
+Notes specific to the BPM formulation:
+
+- The nodal volume must be declared by the user as a :doc:`fix
+  property/atom <fix_property_atom>` named *vfrac* (group *all*, ghost
+  communication on) **before** the bond style is defined.  This is *input*
+  data: it is populated by :doc:`set <set>` (uniform) or :doc:`read_data
+  <read_data>` (per-node) during input parsing, before any *run*, so it
+  cannot be auto-created the way the internal bookkeeping fields are.  The
+  general rule is: input-data per-atom properties are user-declared;
+  purely internal ones (*s0*, *smin*, *vinter*, and the *eps* *lambda*)
+  are auto-created by the bond style.
+- Because the styles never read the mass (only the integrator does), the
+  nodal mass is supplied independently: a uniform per-type :doc:`mass
+  <mass>` equal to density times nodal volume (here :math:`2200 \times
+  1.25\times10^{-10} = 2.75\times10^{-7}`), or, for variable mass,
+  :doc:`atom_style hybrid sphere bond <atom_style>` with per-atom *rmass*.
+- The peridynamic bonds are created with :doc:`create_bonds many
+  <create_bonds>` out to the horizon; *extra/bond/per/atom* must be large
+  enough for the peridynamic coordination number (often 30-60 or more).
+- :doc:`newton <newton>` must be *bond off* and the two-stage
+  *special_bonds* idiom (coul weight 0 during *create_bonds*, then 1) is
+  required, as for all BPM bond styles.
+- When a body fragments, pieces can leave the domain.  The legacy PERI
+  package tolerates lost atoms silently; in the BPM framework this is an
+  explicit, opt-in choice.  To let a shattering simulation continue, use a
+  fixed (non-shrink-wrap) box with margin and, *after* the
+  :doc:`thermo_style <thermo_style>` command (which resets these settings),
+  add ``thermo_modify lost ignore`` and ``thermo_modify lost/bond ignore``;
+  the latter drops the dangling bonds of an atom that has left the domain so
+  the remaining bonds are unaffected.  See the ``examples/bpm/peri`` decks.
+
+Migrating a PERI input to the BPM framework is mostly a one-to-one
+translation:
+
+.. list-table::
+   :header-rows: 1
+   :widths: 50 50
+
+   * - PERI package
+     - BPM framework
+   * - ``atom_style peri``
+     - ``atom_style bond`` (+ ``fix property/atom d_vfrac``)
+   * - ``pair_style peri/pmb`` (+ ``pair_coeff``)
+     - ``pair_style bpm/peri`` + ``bond_style bpm/peri`` (model keyword)
+   * - ``set group all volume V``
+     - ``set group all d_vfrac V``
+   * - ``set group all density D``
+     - ``mass * (D*V)`` (uniform) or per-atom *rmass*
+   * - bonds implicit in the pair neighbor list
+     - explicit ``create_bonds many all all <type> 0.0 <horizon>``
+   * - ``compute damage/atom``
+     - ``fix property/atom d_damage`` + ``compute property/atom d_damage``
+
+The two implementations follow the same constitutive equations.  The
+analytic elastic response (dilatation, energy) agrees; for the *eps*
+model the BPM implementation uses a dimensionally-consistent plastic
+return mapping that is stable under sustained plastic flow.
+
+Performance expectations
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+The BPM implementation is found to be consistently faster than the
+legacy PERI pair styles by a significant marging.  On a periodic
+16x16x16 simple-cubic block (4096 nodes, 122 bonds per node) the
+per-step force cost is roughly 3.6x (pmb), 5.4x (lps), 4.4x (ves) and
+5.9x (eps) lower than the corresponding ``peri/*`` pair style on a
+single MPI rank, and about 4x lower on four ranks.  The legacy styles
+walk a double-counted partner list (each bond visited from both
+endpoints) and combine bond and contact in one pass, whereas the BPM
+bond style visits each bond once and the contact ``pair_style bpm/peri``
+carries a separate, nearly empty short-range list.  The forward
+communication of the per-step dilatation and break state for the
+state-based models is a negligible fraction of the cost.  See
+``examples/bpm/peri/benchmark`` for the input decks.
+
 Peridynamic Model of a Continuum
 """"""""""""""""""""""""""""""""
 
@@ -769,8 +910,12 @@ created for steps 300, 600, and 2000 this way.
 
 |periimage1|  |periimage2|  |periimage3|
 
-For interactive visualization, the `Ovito <https://ovito.org>`_ is very
-convenient to use. Below are steps to create a visualization of the
+For interactive visualization, `OVITO <https://ovito.org>`_ is very
+convenient to use.  As of 2026, many advanced visualizations can now
+also be created with LAMMPS directly using the :doc:`dump image command
+<dump_image>`.  See the :doc:`Howto_viz` page for details.
+
+Below are steps to create a visualization of the
 :ref:`same example from below <periexample>` now using the generated
 trajectory in the ``dump.peri`` file.
 

doc/src/Intro_website.rst

@@ -17,7 +17,7 @@ available online are listed below.
 * `LAMMPS highlights with images <https://www.lammps.org/gallery/pictures/>`_
 * `LAMMPS highlights with movies <https://www.lammps.org/gallery/movies/>`_
 * `Workshops <https://www.lammps.org/workshops/>`_
-* `Tutorials <https://www.lammps.org/tutorials/>`_
+* `Tutorials <https://www.lammps.org/documentation/tutorials/>`_
 
 * `Pre- and post-processing tools for LAMMPS <https://www.lammps.org/ecosystem/prepost/>`_
 * `Other software usable with LAMMPS <https://www.lammps.org/ecosystem/tools/>`_

doc/src/Packages.rst

@@ -338,11 +338,6 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair_style hdnnp <pair_hdnnp>`
      - ``PACKAGES/hdnnp``
      - ext
-   * - :ref:`ML-RUNNER <PKG-ML-RUNNER>`
-     - Second-, third-, and fourth-generation high-dimensional neural network potentials
-     - :doc:`pair_style runner <pair_runner>`
-     - ``PACKAGES/runner``
-     - ext
    * - :ref:`ML-IAP <PKG-ML-IAP>`
      - multiple machine learning potentials
      - :doc:`pair_style mliap <pair_mliap>`
@@ -363,11 +358,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`pair_style quip <pair_quip>`
      - ``PACKAGES/quip``
      - ext
-   * - :ref:`ML-RANN <PKG-ML-RANN>`
-     - Pair style for RANN potentials
-     - :doc:`pair rann <pair_rann>`
-     - ``PACKAGES/rann``
-     - no
+   * - :ref:`ML-RUNNER <PKG-ML-RUNNER>`
+     - Second-, third-, and fourth-generation high-dimensional neural network potentials
+     - :doc:`pair_style runner <pair_runner>`
+     - ``PACKAGES/runner``
+     - ext
    * - :ref:`ML-SNAP <PKG-ML-SNAP>`
      - quantum-fitted potential
      - :doc:`pair_style snap <pair_snap>`