[pull] develop from lammps:develop

.github/release_steps.md

@@ -33,10 +33,14 @@ release and should not contain any other changes. (Exceptions: this
 document, last minute trivial(!) changes).
 
 This PR shall not be merged before **all** pending tests have completed
-and cleared.  We currently use a mix of automated tests running on
-either Temple's Jenkins cluster or GitHub workflows.  Those include time
-consuming tests not run on pull requests.  If needed, a bug-fix pull
-request should be created and merged to clear all tests.
+and cleared.  We currently use automated tests with GitHub workflows.
+There is also a Coverity Scan run with static code analysis done every
+thursday evening or when triggered manually.  That output should be
+checked for any significant issues before a release, too.  In addition
+there is a nightly static code analysis run that can be checked at
+https://downloads.lammps.org/analysis/
+If needed, a bug-fix pull request should be created and merged to clear
+pending issues.
 
 ### Create release on GitHub
 
@@ -45,9 +49,9 @@ cleared testing, the 'next\_release' branch is merged into 'develop'.
 
 Check out or update the 'develop' branch locally, pull the latest
 changes, merge them into 'release' with a fast forward(!) merge, and
-apply a suitable release tag (for historical reasons the tag starts with
-"patch_" followed by the date, and finally push everything back to
-GitHub.  There should be no commits made to 'release' but only
+apply a suitable release tag (for historical reasons the tag starts
+with "patch_" followed by the date, and finally push everything back
+to GitHub.  There should be no commits made to 'release' but only
 fast forward merges.  Example:
 
 ```
@@ -60,17 +64,20 @@ git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
 git push [email protected]:lammps/lammps.git --tags develop release
 ```
 
-Applying this tag will trigger two actions on the Temple Jenkins cluster:
-- The online manual at https://docs.lammps.org/ will be updated to the
+After applying this tag two steps will need to be executed manually
+(they used to be run automatically, but this is currently not available).
+- The online manual at https://docs.lammps.org/ needs to be updated to the
   state of the 'release' branch.  Merges to the 'develop' branch will
   trigger updating https://docs.lammps.org/latest/ so by reviewing the
   version of the manual under the "latest" URL, it is possible to preview
   what the updated release documentation will look like.
 - A downloadable tar archive of the LAMMPS distribution that includes the
-  html format documentation and a PDF of the manual will be created and
-  uploaded to the download server at https://download.lammps.org/tars
+  html format documentation and a PDF of the manual needs to be created
+  and uploaded to the download server at https://download.lammps.org/tars
   Note that the file is added, but the `index.html` file is not updated,
-  so it is not yet publicly visible.
+  so it is not yet publicly visible.  The index file is updated manually
+  with a local script after symlinks and SHASUM files have been updated
+  as well.
 
 Go to https://github.com/lammps/lammps/releases and create a new (draft)
 release page with a summary of all the changes included and references
@@ -81,9 +88,17 @@ a tag" drop-down list. Go to the bottom of the list and select the "Set
 as pre-release" checkbox.  The "Set as the latest release" button is
 reserved for stable releases and updates to them.
 
-If everything is in order, you can click on the "Publish release"
-button.  Otherwise, click on "Save draft" and finish pending tasks until
-you can return to edit the release page and publish it.
+Releases are now "immutable", so neither the tag hash nor any uploaded
+assets can be changed after the release is published.  Only the
+release notes text may be changed, e.g. to document issues with the
+uploaded assets.
+
+Thus only when *everything* is in order *and* all required assets (source,
+binary packages for different platforms, manual PDF) are uploaded in
+a suitable version, you can click on the "Publish release" button.
+Otherwise, click on "Save draft" and finish pending tasks until you can
+return to edit the release page, update assets, and publish it when
+it is ready.
 
 ### Prepare pre-compiled packages, update packages to GitHub
 

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "10 September 2025" "2025-09-10"
+.TH LAMMPS "1" "10 December 2025" "2025-12-10"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 10 September 2025
+\- Molecular Dynamics Simulator.  Version 10 Decmber 2025
 
 .SH SYNOPSIS
 .B lmp

doc/src/Commands_fix.rst

@@ -274,6 +274,7 @@ OPT.
    * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`
+   * :doc:`wall/harmonic/outside <fix_wall>`
    * :doc:`wall/lj1043 <fix_wall>`
    * :doc:`wall/lj126 <fix_wall>`
    * :doc:`wall/lj93 (k) <fix_wall>`

doc/src/Developer_unittest.rst

@@ -147,7 +147,7 @@ additional tests.
 FFT Testing Infrastructure
 """"""""""""""""""""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 The FFT tests (``test_fft3d.cpp`` and ``test_fft3d_kokkos.cpp``)
 validate the LAMMPS FFT wrapper implementations for both standard (CPU)

doc/src/compute_reduce.rst

@@ -243,18 +243,20 @@ scalar or vector values from a compute as input.  See the :doc:`Howto
 output <Howto_output>` doc page for an overview of LAMMPS output
 options.
 
+.. versionadded:: 10Dec2025
+
 This compute supports automatically generated thermo column names when
 using :doc:`thermo_modify colname auto <thermo_modify>`.  The thermo column
-names are 'c_', followed by the compute ID, followed by a colon, followed
+names are "c\_", followed by the compute ID, followed by a colon, followed
 by the reduction operation (*mode*), followed by the compute being operated
 on in parentheses.  E.g., for the first in-text example above, the first
-printed thermo column name would be 'c_2:min(c_myPress[1])', rather than
-the default 'c_2[1]'.  If the *replace* keyword is used, *vec1* of the
+printed thermo column name would be "c\_2:min(c_myPress[1])", rather than
+the default "c\_2[1]".  If the *replace* keyword is used, *vec1* of the
 *replace* keyword is listed after the colon, followed by '<-', followed by
 the reduction operation, followed by *vec2* of the *replace* keyword in
 parentheses.  E.g., for the second in-text example above, the first printed
-thermo column name would be 'c_3:c_batoms[1]<-max(c_blength)' rather than
-the default 'c_3[1]'.
+thermo column name would be "c\_3:c\_batoms[1]<-max(c\_blength)" rather than
+the default "c\_3[1]".
 
 All the scalar or vector values calculated by this compute are
 "intensive", except when the *sum*, *sumabs*, or *sumsq* modes are used on

doc/src/fix.rst

@@ -453,6 +453,7 @@ accelerated styles exist.
 * :doc:`wall/gran <fix_wall_gran>` - frictional wall(s) for granular simulations
 * :doc:`wall/gran/region <fix_wall_gran_region>` - :doc:`fix wall/region <fix_wall_region>` equivalent for use with granular particles
 * :doc:`wall/harmonic <fix_wall>` - harmonic spring wall
+* :doc:`wall/harmonic/outside <fix_wall>` - harmonic spring wall for containing particles
 * :doc:`wall/lj1043 <fix_wall>` - Lennard-Jones 10--4--3 wall
 * :doc:`wall/lj126 <fix_wall>` - Lennard-Jones 12--6 wall
 * :doc:`wall/lj93 <fix_wall>` - Lennard-Jones 9--3 wall

doc/src/fix_addtorque_atom.rst

@@ -39,7 +39,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 This fix is intended to add a peratom torque of each individual
 finite-sized atom in the group to the specified values. Unlike

doc/src/fix_addtorque_group.rst

@@ -26,7 +26,7 @@ Examples
 Description
 """""""""""
 
-.. versionchanged:: TBD
+.. versionchanged:: 10Dec2025
    Fix *addtorque* was renamed to fix *addtorque/group*
 
 Add a set of forces to each atom in

doc/src/fix_align_self.rst

@@ -34,7 +34,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 Add a torque to each atom in the group due to a self-alignment toward an
 intrinsic orientation. The torque is given by :
@@ -122,7 +122,7 @@ Related commands
 
 :doc:`fix propel/self <fix_propel_self>`,
 :doc:`fix brownian <fix_brownian>`,
-:doc:`fix addtorque <fix_addtorque>`
+:doc:`fix addtorque/group <fix_addtorque_group>`
 
 Default
 """""""

doc/src/fix_atom_swap.rst

@@ -49,17 +49,27 @@ atoms of the other given atom types.  The specified scaling temperature
 *T* is used in the Metropolis criterion dictating swap probabilities.
 
 Perform *X* swaps of atoms of one type with atoms of another type
-according to a Monte Carlo probability. Swap candidates must be in the
-fix group, must be in the region (if specified), and must be of one of
-the listed types. Swaps are attempted between candidates that are chosen
-randomly with equal probability among the candidate atoms. Swaps are not
-attempted between atoms of the same type since nothing would happen.
-
-All atoms in the simulation domain can be moved using regular time
-integration displacements (e.g., via :doc:`fix nvt <fix_nh>`), resulting
-in a hybrid MC+MD simulation. A smaller-than-usual timestep size may be
-needed when running such a hybrid simulation, especially if the swapped
-atoms are not well equilibrated.
+according to a Monte Carlo probability.  Swap candidates must be in
+the fix group, must be in the region (if specified), and must be of
+one of the listed types. Swaps are attempted between candidates that
+are chosen randomly with equal probability among the candidate
+atoms. Swaps are not attempted between atoms of the same type since
+nothing would happen.
+
+All atoms in the simulation domain can also be moved using regular
+time integration displacements (e.g., via :doc:`fix nvt <fix_nh>`),
+resulting in a hybrid MC+MD simulation, where $X$ MC swap attempts are
+made once every $N$ MD steps.  A smaller-than-usual timestep size may
+be needed when running such a hybrid simulation, especially if the
+swapped atoms are not well equilibrated.
+
+.. note::
+
+   To run an MC-only simulation (no MD), you should define no
+   time-integration fix, set the :doc:`thermo <thermo>` command to 1,
+   set *N* to 1, and set *X* small enough to see the MC evolution of
+   the system.  But if *X* is too small, the overhead at the start and
+   stop of MC moves each timestep will slow down the simulation.
 
 The *types* keyword is required. At least two atom types must be
 specified. If not using *semi-grand*, exactly two atom types are

doc/src/fix_bond_react.rst

@@ -836,12 +836,14 @@ There is one quantity in the global vector for each *react* argument:
 
   (1) cumulative number of reactions that occurred
 
+.. versionadded:: 10Dec2025
+
 This fix supports automatically generated thermo column names when using
 :doc:`thermo_modify colname auto <thermo_modify>`.  The thermo column names
-are 'f_', followed by the fix ID, followed by a colon, followed by the
+are "f\_", followed by the fix ID, followed by a colon, followed by the
 react-ID.  E.g., the first example in the Examples section above would
-print a thermo column name of 'f_rxns:diels_alder', compared to the default column
-output name of 'f_rxns[1]'.
+print a thermo column name of "f\_rxns:diels_alder", compared to the default column
+output name of "f\_rxns[1]".
 
 No parameter of this fix can be used with the *start/stop* keywords
 of the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.

doc/src/fix_gcmc.rst

@@ -1,3 +1,4 @@
+
 .. index:: fix gcmc
 
 fix gcmc command
@@ -80,22 +81,30 @@ isotherms in microporous materials, or computing vapor-liquid
 coexistence curves.
 
 Every *N* timesteps the fix attempts both GCMC exchanges (insertions or
-deletions) and MC moves of gas atoms or molecules.  On those timesteps,
-the average number of attempted GCMC exchanges is *X*, while the average
-number of attempted MC moves is *M*.  For GCMC exchanges of either
-molecular or atomic gasses, these exchanges can be either deletions or
-insertions, with equal probability.
-
-The possible choices for MC moves are translation of an atom,
-translation of a molecule, and rotation of a molecule.  The relative
-amounts of each are determined by the optional *mcmoves* keyword (see
-below).  The default behavior is as follows.  If the *mol* keyword is
-used, only molecule translations and molecule rotations are performed
-with equal probability.  Conversely, if the *mol* keyword is not used,
-only atom translations are performed.  *M* should typically be chosen to
-be approximately equal to the expected number of gas atoms or molecules
-of the given type within the simulation cell or region, which will
-result in roughly one MC move per atom or molecule per MC cycle.
+deletions) and MC moves of gas atoms or molecules.  On those timesteps, the
+average number of attempted GCMC exchanges is *X*, while the average number
+of attempted MC moves is *M*.  For GCMC exchanges of either molecular or
+atomic gasses, these exchanges can be either deletions or insertions, with
+equal probability.
+
+.. note::
+
+   To run an MC-only simulation (no MD), you should define no
+   time-integration fix, set the :doc:`thermo <thermo>` command to 1,
+   set *N* to 1, and set *X+M* small enough to see the MC evolution of
+   the system.  But if *X+M* is too small, the overhead at the start
+   and stop of MC moves each timestep will slow down the simulation.
+
+The possible choices for MC moves are translation of an atom, translation
+of a molecule, and rotation of a molecule.  The relative amounts of each are
+determined by the optional *mcmoves* keyword (see below).  The default
+behavior is as follows. If the *mol* keyword is used, only molecule
+translations and molecule rotations are performed with equal probability.
+Conversely, if the *mol* keyword is not used, only atom translations are
+performed.  *M* should typically be chosen to be approximately equal to the
+expected number of gas atoms or molecules of the given type within the
+simulation cell or region, which will result in roughly one MC move per
+atom or molecule per MC cycle.
 
 All inserted particles are always added to two groups: the default group
 "all" and the fix group specified in the fix command.  In addition,

doc/src/fix_neighbor_swap.rst

@@ -97,6 +97,14 @@ The algorithm implemented by this fix is as follows:
      using the energy change of the system and the specified temperature
      *T*.
 
+.. note::
+
+   To run an MC-only simulation (no MD), you should define no
+   time-integration fix, set the :doc:`thermo <thermo>` command to 1,
+   set *N* to 1, and set *X* small enough to see the MC evolution of
+   the system.  But if *X* is too small, the overhead at the start and
+   stop of MC moves each timestep will slow down the simulation.
+
 Here are a few comments on the computational cost of the swapping
 algorithm.
 

doc/src/fix_nh.rst

@@ -642,14 +642,16 @@ by tchain for eta_dot, followed by ndof for omega, etc:
 * KE_etap_dot[pchain] = kinetic energy of each barostat thermostat velocity (energy units)
 * PE_strain[1] = scalar strain energy (energy units)
 
+.. versionadded:: 10Dec2025
+
 This fix supports automatically generated thermo column names when using
 :doc:`thermo_modify colname auto <thermo_modify>`.  The thermo column names
-are 'f_', followed by the fix ID, followed by a colon, followed by a
+are "f\_", followed by the fix ID, followed by a colon, followed by a
 keyword listed above, followed by an index for that keyword.  Indices range
 from 1 to the number of values for that keyword.  E.g., the first example
 in the Examples section above would print a thermo column name of
-'f_1:eta[1]', compared to the default column output name of 'f_1[1]'.
-Similarly, f_1:eta_dot[1] would be printed instead of the default 'f_1[4]'.
+"f\_1:eta[1]", compared to the default column output name of "f\_1[1]".
+Similarly, "f\_1:eta_dot[1]" would be printed instead of the default "f\_1[4].
 
 These fixes can ramp their external temperature and pressure over
 multiple runs, using the *start* and *stop* keywords of the

doc/src/fix_pimd.rst

@@ -244,7 +244,7 @@ support for bosonic normal modes.
    (:math:`\sum_{i=1}^P \frac{1}{2}m\omega_P^2(q_i - q_{i+1})^2`, :math:`m` is always the
    actual mass of the particles).
 
-.. versionchanged:: TBD
+.. versionchanged:: 10Dec2025
 
    *sp* keyword added to *fix pimd/langevin*
 

doc/src/fix_reaxff_species.rst

@@ -160,7 +160,7 @@ an equal-style :doc:`variable <variable>`. When using the
 first Nsteps timesteps of the first run (after reading either a data or
 restart file).
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 The *delete_subgroup* keyword enforces a requirement that deleted molecules
 must have at least one atom in the group specified by the keyword's

doc/src/fix_settorque_atom.rst

@@ -34,7 +34,7 @@ Examples
 Description
 """""""""""
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 This fix is intended to set the peratom torque of individual finite-size
 atoms in the fix group to the specified values. Unlike :doc:`fix
@@ -80,10 +80,10 @@ to it.
    This fix is not (currently) designed to be used with rigid fixes.
    While it will set the torque of all of the atoms in a rigid body as
    described above, there is not always an easy mapping between these
-   peratom torques and the torque experienced by the body. The exception
-   may be when used in conjunction to :doc:`fix setforce <set_force>` to
-   simultaneously zero forces and torques to freeze a rigid body.
-
+   peratom torques and the torque experienced by the body.  The exception
+   may be when it is used in conjunction with
+   :doc:`fix setforce <fix_setforce>` to simultaneously zero forces and
+   torques to freeze a rigid body.
 
 ----------
 

doc/src/fix_shake.rst

@@ -204,7 +204,7 @@ will be fulfilled to the desired accuracy within a few MD steps
 following the minimization. The default value for *kbond* depends on the
 :doc:`units <units>` setting and is 1.0e9*k_B.
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 The *store* keyword controls whether the fix stores the constraint
 (or restraint) forces as a per-atom property.

doc/src/fix_srd.rst

@@ -295,7 +295,7 @@ big particles or walls have a thermostatting effect on the colliding particles,
 so it may not be necessary to thermostat the SRD particles on a bin by bin
 basis in that case.
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 The *unbiased* keyword controls how the thermostat operates if there is a streaming
 velocity associated with the system, e.g. due to use of the

doc/src/fix_store_state.rst

@@ -64,7 +64,7 @@ Syntax
        *com* value = *yes* or *no*
        *thresh* args = variable operator value
          variable = equal style or compatible variable reference
-         operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "|^"
+         operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|^"
          value = numeric value to compare to
 
 
@@ -111,7 +111,7 @@ If the *com* keyword is set to *yes* then the *xu*, *yu*, and *zu*
 inputs store the position of each atom relative to the center-of-mass
 of the group of atoms, instead of storing the absolute position.
 
-.. versionadded:: TBD
+.. versionadded:: 10Dec2025
 
 If the *thresh* keyword is used, data is only stored on steps where also
 the threshold condition following the keyword is met.  The first