Merge branch 'develop' into remove-smallsmall

cmake/presets/kokkos-cuda.cmake

@@ -1,6 +1,5 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. This preselects CC 5.0 as default GPU arch, since
+# enabled as well. The GPU architecture *must* match your hardware
-# that is compatible with all higher CC, but not the default CC 3.5
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)

doc/src/Commands_fix.rst

@@ -162,8 +162,8 @@ OPT.
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd/langevin <fix_pimd>`
    * :doc:`pimd/nvt <fix_pimd>`
-   * :doc:`pimd/langevin/bosonic <fix_pimd_bosonic>`
+   * :doc:`pimd/langevin/bosonic <fix_pimd>`
-   * :doc:`pimd/nvt/bosonic <fix_pimd_bosonic>`
+   * :doc:`pimd/nvt/bosonic <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`

doc/src/Commands_removed.rst

@@ -170,6 +170,18 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
 and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
+Compute atom/molecule
+_____________________
+
+.. deprecated:: 11 Dec2015
+
+The atom/molecule command has been removed from LAMMPS since it was superseded
+by the more general and extensible "chunk infrastructure".  Here the system is
+partitioned in one of many possible ways - including using molecule IDs -
+through the :doc:`compute chunk/atom <compute_chunk_atom>` command and then
+summing is done using :doc:`compute reduce/chunk <compute_reduce_chunk>` Please
+refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
+
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 

doc/src/Developer.rst

@@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community.
    Classes
    Developer_platform
    Developer_utils
+   Developer_internal
    Developer_grid

doc/src/Developer_internal.rst

@@ -0,0 +1,113 @@
+
+Internal Styles
+---------------
+
+LAMMPS has a number of styles that are not meant to be used in an input
+file and thus are not documented in the :doc:`LAMMPS command
+documentation <Commands_all>`.  The differentiation between user
+commands and internal commands is through the case of the command name:
+user commands and styles are all lower case, internal styles are all
+upper case.  Internal styles are not called from the input file, but
+their classes are instantiated by other styles.  Often they are
+created by other styles to store internal data or to perform actions
+regularly at specific steps of the simulation.
+
+The paragraphs below document some of those styles that have general
+utility and may be used to avoid redundant implementation.
+
+DEPRECATED Styles
+^^^^^^^^^^^^^^^^^
+
+The styles called DEPRECATED (e.g. pair, bond, fix, compute, region, etc.)
+have the purpose to inform users that a specific style has been removed
+or renamed.  This is achieved by creating an alias for the deprecated
+style to the corresponding class.  For example, the fix style DEPRECATED
+is aliased to fix style ave/spatial and fix style ave/spatial/sphere with
+the following code:
+
+.. code-block:: c++
+
+   FixStyle(DEPRECATED,FixDeprecated);
+   FixStyle(ave/spatial,FixDeprecated);
+   FixStyle(ave/spatial/sphere,FixDeprecated);
+
+The individual class will then determine based on the style name
+what action to perform:
+
+- inform that the style has been removed and what style replaces it, if any, and then error out
+- inform that the style has been renamed and then either execute the replacement or error out
+- inform that the style is no longer required, and it is thus ignored and continue
+
+There is also a section in the user's guide for :doc:`removed commands
+and packages <Commands_removed>` with additional explanations.
+
+Internal fix styles
+^^^^^^^^^^^^^^^^^^^
+
+fix DUMMY
+"""""""""
+
+Most fix classes cannot be instantiated before the simulation box has
+been created since they access data that is only available then.
+However, in some cases it is required that a fix must be at or close to
+the top of the list of all fixes.  In those cases an instance of the
+DUMMY fix style may be created by calling ``Modify::add_fix()`` and then
+later replaced by calling ``Modify::replace_fix()``.
+
+fix STORE/ATOM
+""""""""""""""
+
+Fix STORE/ATOM can be used as persistent storage of per-atom data.
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/ATOM N1 N2 gflag rflag
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/ATOM = style name of this fix command
+* N1 = 1, N2 = 0 : data is per-atom vector = single value per atom
+* N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom
+* N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom
+* gflag = 1 communicate per-atom values with ghost atoms, 0 do not update ghost atom data
+* rflag = 1 store per-atom value in restart file, 0 do not store data in restart
+
+Similar functionality is also available through using custom per-atom
+properties with :doc:`fix property/atom <fix_property_atom>`.  The
+choice between the two fixes should be based on whether the user should
+be able to access this per-atom data: if yes, then fix property/atom is
+preferred, otherwise fix STORE/ATOM.
+
+fix STORE/GLOBAL
+""""""""""""""""
+
+Fix STORE/GLOBAL can be used as persistent storage of global data with support for restarts
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/GLOBAL N1 N2
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/GLOBAL = style name of this fix command
+* N1 >=1 : number of global items to store
+* N2 = 1 : data is global vector of length N1
+* N2 > 1 : data is global N1xN2 array
+
+fix STORE/LOCAL
+"""""""""""""""
+
+Fix STORE/LOCAL can be used as persistent storage for local data
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/LOCAL Nreset Nvalues
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/LOCAL = style name of this fix command
+* Nreset = frequency at which local data is available
+* Nvalues = number of values per local item, that is the number of columns

doc/src/Errors_details.rst

@@ -8,16 +8,7 @@ not the exact cause, or where the explanation needs to be more detailed
 than what can be fit into a message printed by the program.  The
 following are discussions of such cases.
 
-- :ref:`Unknown identifier in data file <err0001>`
+.. contents::
-- :ref:`Incorrect format in ... section of data file <err0002>`
-- :ref:`Illegal variable command: expected X arguments but found Y <err0003>`
-- :ref:`Out of range atoms - cannot compute ... <err0004>`
-- :ref:`Too many neighbor bins <err0009>`
-- :ref:`Cannot use neighbor bins - box size \<\< cutoff <err0015>`
-- :ref:`Domain too large for neighbor bins <err0017>`
-- :ref:`Molecule topology/atom exceeds system topology/atom <err0024>`
-- :ref:`Molecule topology type exceeds system topology type <err0025>`
-- :ref:`Molecule attributes do not match system attributes <err0026>`
 
 ------
 
@@ -27,6 +18,8 @@ General troubleshooting advice
 Below are suggestions that can help to understand the causes of problems
 with simulations leading to errors or unexpected results.
 
+.. _hint01:
+
 Create a small test system
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -36,6 +29,8 @@ a small test system input that has the same issue, but will take much
 time until it triggers the error condition.  Also, it will be easier to
 see what happens.
 
+.. _hint02:
+
 Visualize your trajectory
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -46,6 +41,8 @@ avoid gigantic files, you can use :doc:`dump_modify delay <dump_modify>`
 to delay output until the critical section is reached, and you can use a
 smaller test system (see above).
 
+.. _hint03:
+
 Parallel versus serial
 ^^^^^^^^^^^^^^^^^^^^^^
 
@@ -55,16 +52,49 @@ only the symptoms are not triggering an error quickly.  Correspondingly,
 errors may be triggered faster with more processors and thus smaller
 sub-domains.
 
+.. _hint04:
+
+Segmentation Fault
+^^^^^^^^^^^^^^^^^^
+
+A segmentation fault is an error reported by the **operating system**
+and not LAMMPS itself.  It happens when a process tries to access a
+memory address that is not available.  This can have **many** reasons:
+memory has not been allocated, a memory buffer is not large enough, a
+memory address is computed from an incorrect index, a memory buffer is
+used after it has been freed, some general memory corruption.  When
+investigating a segmentation fault (aka segfault), it is important to
+determine which process is causing it; it may not always be LAMMPS.  For
+example, some MPI library implementations report a segmentation fault
+from their "mpirun" or "mpiexec" command when the application has been
+terminated unexpectedly.
+
+While a segmentation fault is likely an indication of a bug in LAMMPS,
+it need not always be; it can also be the consequence of too aggressive
+simulation settings.  For time critical code paths, LAMMPS will assume
+the user has chosen the settings carefully and will not make any checks
+to avoid to avoid performance penalties.
+
+A crucial step in resolving a segmentation fault is to identify the exact
+location in the code where it happens.  Please see `Errors_debug` for
+a couple of examples showing how to do this on a Linux machine.  With
+this information -- a simple way to reproduce the segmentation fault and
+the exact :doc:`LAMMPS version <Manual_version>` and platform you are
+running on -- you can contact the LAMMPS developers or post in the LAMMPS
+forum to get assistance.
+
+.. _hint05:
+
 Fast moving atoms
 ^^^^^^^^^^^^^^^^^
 
 Fast moving atoms may be "lost" or "missing" when their velocity becomes
 so large that they can cross a sub-domain within one timestep.  This
 often happens when atoms are too close, but atoms may also "move" too
-fast from sub-domain to sub-domain if the box changes rapidly, e.g. when
+fast from sub-domain to sub-domain if the box changes rapidly. E.g. when
 setting a large an initial box with :doc:`shrink-wrap boundary
 conditions <boundary>` that collapses on the first step (in this case
-the solution is often using 'm' instead of 's' as boundary condition).
+the solution is often using 'm' instead of 's' as a boundary condition).
 
 To reduce the impact of "close contacts", one can remove those atoms or
 molecules with something like :doc:`delete_atoms overlap 0.1 all all
@@ -74,16 +104,28 @@ to first run a minimization (aka quench) before starting the MD.  Reducing
 the time step can also help.  Many times, one just needs to "ease" the
 system into a balanced state and can then switch to more aggressive settings.
 
-The speed of atoms during an MD depends on the steepness of the
+The speed of atoms during an MD run depends on the steepness of the
 potential function and their mass.  Since the positions and velocities
-of atoms are computed with finite timesteps, they choice of timestep can
+of atoms are computed with finite timesteps, the timestep needs to be
-be too large for a stable numeric integration of the trajectory.  In
+small enough for stable numeric integration of the trajectory.  If the timestep
-those cases using (temporarily) :doc:`fix nve/limit <fix_nve_limit>` or
+is too large during initialization (or other instances of extreme dynamics),
-:doc:`fix dt/reset <fix_dt_reset>` can help to avoid too large updates
+using :doc:`fix nve/limit <fix_nve_limit>` or :doc:`fix dt/reset <fix_dt_reset>`
-or adapt the timestep according to the displacements.
+temporarily can help to avoid too large updates or adapt the timestep according
+to the displacements.
 
+.. _hint06:
 
-Pressure, forces, positions becoming NaN of Inf
+Ignoring lost atoms
+^^^^^^^^^^^^^^^^^^^
+
+It is tempting to use the :doc:`thermo_modify lost ignore <thermo_modify>`
+to avoid LAMMPS aborting with an error on lost atoms.  This setting should,
+however, *only* be used when atoms *should* leave the system.  In general,
+ignoring a problem does not solve it.
+
+.. _hint07:
+
+Pressure, forces, positions becoming NaN or Inf
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Some potentials can overflow or have a division by zero with close contacts
@@ -99,24 +141,28 @@ package it may be beneficial to run with double precision initially before
 switching to mixed or single precision for faster execution when the system
 has relaxed.
 
+.. _hint08:
+
 Communication cutoff
 ^^^^^^^^^^^^^^^^^^^^
 
 The communication cutoff determines the "overlap" between sub-domains
 and atoms in these regions are referred to in LAMMPS as "ghost atoms".
 This region has to be large enough to contain all atoms of a bond,
-angle, dihedral or improper with just one atom in the actual sub-domain.
+angle, dihedral, or improper with just one atom in the actual sub-domain.
 Typically, this cutoff is set to the largest cutoff from the :doc:`pair
 style(s) <pair_style>` plus the :doc:`neighbor list skin distance
-<neighbor>` and will be more than sufficient for all bonded
+<neighbor>` and will typically be sufficient for all bonded
-interactions.  But if the pair style cutoff is small this may bot be
+interactions.  But if the pair style cutoff is small, this may not be
 enough.  LAMMPS will print a warning in this case using some heuristic
-based on the equilibrium bond length, but that may not be sufficient for
+based on the equilibrium bond length, but that still may not be sufficient
-cases where the force constants are small and thus bonds may be
+for cases where the force constants are small and thus bonds may be
 stretched very far.  The communication cutoff can be adjusted with
 :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this too
 large will waste CPU time and memory.
 
+.. _hint09:
+
 Neighbor list settings
 ^^^^^^^^^^^^^^^^^^^^^^
 
@@ -125,16 +171,10 @@ for "lost" or "missing" atoms.  Thus it can help to use very
 conservative :doc:`neighbor list settings <neigh_modify>` and then
 examine the neighbor list statistics if the neighbor list rebuild can be
 safely delayed.  Rebuilding the neighbor list less frequently
-(i.e. through increasing the *delay* or *every* setting has diminishing
+(i.e. through increasing the *delay* or *every*) setting has diminishing
-returns and increasing risks).
+returns and increasing risks.
 
-Ignoring lost atoms
+.. _hint10:
-^^^^^^^^^^^^^^^^^^^
-
-It is tempting to use the :doc:`thermo_modify lost ignore <thermo_modify>`
-to avoid that LAMMPS stops with an error.  This setting should, however,
-*only* be used when atoms *should* leave the system.  In general, ignoring
-a problem does not solve it.
 
 Units
 ^^^^^
@@ -151,23 +191,48 @@ are parameterized for other settings, most notably :doc:`ReaxFF
 potentials <pair_reaxff>` that use "real" units.
 
 Also, individual parameters for :doc:`pair_coeff <pair_coeff>` commands
-taken from publications or other MD software, may need to be converted
+taken from publications or other MD software may need to be converted
 and sometimes in unexpected ways.  Thus some careful checking is
 recommended.
 
+.. _hint11:
+
 No error message printed
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-In some cases - especially when running in parallel with MPI - LAMMPS
+In some cases -- especially when running in parallel with MPI -- LAMMPS
-may stop without displaying an error.  But that does not mean, that
+may stop without displaying an error.  But the fact that nothing was
-there was no error message, instead it is highly likely that the message
+displayed does not mean there was not an error message. Instead it is
-was written to a buffer and LAMMPS was aborted before the buffer was
+highly likely that the message was written to a buffer and LAMMPS was
-output.  Usually, output buffers are output for every line of output,
+aborted before the buffer was output.  Usually, output buffers are output
-but sometimes, this is delayed until 4096 or 8192 bytes of output have
+for every line of output, but sometimes this is delayed until 4096 or
-been accumulated.  This buffering for screen and logfile output can be
+8192 bytes of output have been accumulated.  This buffering for screen
-disabled by using the :ref:`-nb or -nonbuf <nonbuf>` command-line flag.
+and logfile output can be disabled by using the :ref:`-nb or -nonbuf
-This is most often needed when debugging crashing multi-replica
+<nonbuf>` command-line flag. This is most often needed when debugging
-calculations.
+crashing multi-replica calculations.
+
+.. _hint12:
+
+Errors before or after the simulation box is created
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As critical step in a LAMMPS input is when the simulation box is
+defined, either with a :doc:`create_box command <create_box>`, a
+:doc:`read_data command <read_data>`, or a :doc:`read_restart command
+<read_restart>`.  After this step, certain settings are locked in (e.g.
+units, or number of atom, bond, angle, dihedral, improper types) and
+cannot be changed after that.  Consequently, commands that change such
+settings (e.g. :doc:`units <units>`) are only allowed before the box is
+defined.  Very few commands can be used before and after, like
+:doc:`pair_style <pair_style>` (but not :doc:`pair_coeff <pair_coeff>`).
+Most LAMMPS commands must be used after the simulation box is created.
+
+Consequently, LAMMPS will stop with an error, if a command is used in
+the wrong place.  This is not always obvious. So index or string style
+:doc:`variables <variable>` can be expanded anywhere in the input, but
+equal style (or similar) variables can only be expanded before the box
+is defined if they do not reference anything that cannot be defined
+before the box (e.g. a compute or fix reference or a thermo keyword).
 
 ------
 
@@ -197,8 +262,8 @@ treated as a comment.
 Another possibility to trigger this error is to have a keyword in the
 data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
 but the :doc:`read_data <read_data>` command is missing the (optional)
-arguments that identify the fix and the header keyword and section
+arguments that identify the fix and its header and section keywords.
-keyword or those arguments are inconsistent with the keywords in the
+Alternatively, those arguments are inconsistent with the keywords in the
 data file.
 
 .. _err0002:
@@ -208,63 +273,61 @@ Incorrect format in ... section of data file
 
 This error happens when LAMMPS reads the contents of a section of a
 :doc:`data file <read_data>` and the number of parameters in the line
-differs from what is expected.  This most commonly happens, when the
+differs from what is expected.  This most commonly happens when the
 atom style is different from what is expected for a specific data file
 since changing the atom style usually changes the format of the line.
 
-This error can also happen when the number of entries indicated in the
+This error can also occur when the number of entries indicated in the
 header of a data file (e.g. the number of atoms) is larger than the
 number of lines provided (e.g. in the corresponding Atoms section)
-and then LAMMPS will continue reading into the next section and that
+causing LAMMPS to continue reading into the next section which has
-would have a completely different format.
+a completely different format.
 
 .. _err0003:
 
 Illegal variable command: expected X arguments but found Y
 ----------------------------------------------------------
 
-This error indicates that there are the wrong number of arguments for a
+This error indicates that a variable command has the wrong number of
-specific variable command, but a common reason for that is a variable
+arguments. A common reason for this is that the variable expression
-expression that has whitespace but is not enclosed in single or double
+has whitespace, but is not enclosed in single or double quotes.
-quotes.
 
 To explain, the LAMMPS input parser reads and processes lines.  The
 resulting line is broken down into "words".  Those are usually
-individual commands, labels, names, values separated by whitespace (a
+individual commands, labels, names, and values separated by whitespace (a
 space or tab character).  For "words" that may contain whitespace, they
 have to be enclosed in single (') or double (") quotes.  The parser will
-then remove the outermost pair of quotes and then pass that string as
+then remove the outermost pair of quotes and pass that string as
 "word" to the variable command.
 
-Thus missing quotes or accidental extra whitespace will lead to the
+Thus missing quotes or accidental extra whitespace will trigger this
-error shown in the header because the unquoted whitespace will result
+error because the unquoted whitespace will result in the text being broken
-in the text being broken into more "words", i.e. the variable expression
+into more "words", i.e. the variable expression being split.
-being split.
 
 .. _err0004:
 
 Out of range atoms - cannot compute ...
 ---------------------------------------
 
-The PPPM (and also PPPMDisp and MSM) methods require to assemble a grid
+The PPPM (and also PPPMDisp and MSM) methods need to assemble a grid
 of electron density data derived from the (partial) charges assigned to
-the atoms.  This charges are smeared out across multiple grid points
+the atoms.  These charges are smeared out across multiple grid points
 (see :doc:`kspace_modify order <kspace_modify>`).  When running in
 parallel with MPI, LAMMPS uses a :doc:`domain decomposition scheme
 <Developer_par_part>` where each processor manages a subset of atoms and
-thus also a grid representing the density, which covers the actual
+thus also a grid representing the density. The processor's grid covers the
-volume of the sub-domain and some extra space corresponding to the
+actual volume of the sub-domain and some extra space corresponding to the
 :doc:`neighbor list skin <neighbor>`.  These are then :doc:`combined and
 redistributed <Developer_par_long>` for parallel processing of the
 long-range component of the Coulomb interaction.
 
-The ``Out of range atoms`` error can happen, when atoms move too fast or
+The ``Out of range atoms`` error can happen when atoms move too fast,
-the neighbor list skin is too small or the neighbor lists are not
+the neighbor list skin is too small, or the neighbor lists are not
-updated frequently enough.  Then the smeared charges cannot be fully
+updated frequently enough.  The smeared charges cannot then be fully
 assigned to the density grid for all atoms.  LAMMPS checks for this
 condition and stops with an error.  Most of the time, this is an
-indication of a system with very high forces, most often at the
+indication of a system with very high forces, often at the beginning
-beginning of a simulation or when boundary conditions are changed.  The
+of a simulation or when boundary conditions are changed.  The
 error becomes more likely with more MPI processes.
 
 There are multiple options to explore for avoiding the error.  The best
@@ -272,13 +335,73 @@ choice depends strongly on the individual system, and often a
 combination of changes is required.  For example, more conservative MD
 parameter settings can be used (larger neighbor skin, shorter time step,
 more frequent neighbor list updates).  Sometimes, it helps to revisit
-the system generation and avoid close contacts when building it, or use
+the system generation and avoid close contacts when building it. Otherwise
-the :doc:`delete_atoms overlap<delete_atoms>` command to delete those
+one can use the :doc:`delete_atoms overlap<delete_atoms>` command to delete
-close contact atoms, or run a minimization before the MD.  It can also
+those close contact atoms or run a minimization before the MD.  It can also
 help to temporarily use a cutoff-Coulomb pair style and no kspace style
 until the system has somewhat equilibrated and then switch to the
 long-range solver.
 
+.. _err0005:
+
+Bond (or angle, dihedral, or improper) atoms missing
+----------------------------------------------------
+
+The second atom needed to compute a particular bond (or the third or fourth
+atom for angle, dihedral, or improper) is missing on the indicated timestep
+and processor. Typically, this is because the two bonded atoms have become
+too far apart relative to the communication cutoff distance for ghost atoms.
+By default, the communication cutoff is set by the pair cutoff. However, to
+accommodate larger distances between topologically connected atoms, it can
+be manually adjusted using :doc:`comm_modify <comm_modify>` at the cost of
+increased communication and more ghost atoms. However, missing bond atoms
+may also indicate that there are unstable dynamics which caused the atoms
+to blow apart. In this scenario, increasing the communication distance will
+not solve the underlying issue. Rather, see :ref:`Fast moving atoms <hint05>`
+and :ref:`Neighbor list settings <hint09>` in the general troubleshooting
+section above for ideas to fix unstable dynamics.
+
+If atoms are intended to be lost during a simulation (e.g. due to open boundary
+conditions or :doc:`fix evaporate <fix_evaporate>`) such that two bonded atoms
+may be lost at different times from each other, this error can be converted to a
+warning or turned off using the *lost/bond* keyword in the :doc:`thermo_modify
+<thermo_modify>` command.
+
+.. _err0006:
+
+Non-numeric atom coords - simulation unstable
+---------------------------------------------
+This error usually occurs due to issues with system geometry or the potential in
+use. See :ref:`Pressure, forces, positions becoming NaN or Inf <hint07>` above in the
+general troubleshooting section.
+
+.. _err0007:
+
+Non-numeric pressure - simulation unstable
+------------------------------------------
+This error usually occurs due to issues with system geometry or the potential in
+use. See :ref:`Pressure, forces, positions becoming NaN or Inf <hint07>` above in the
+general troubleshooting section.
+
+
+.. _err0008:
+
+Lost atoms ...
+--------------
+
+A simulation stopping with an error due to lost atoms can have multiple
+causes. In the majority of cases, lost atoms are unexpected and a result
+of extremely high velocities causing instabilities in the system, and
+those velocities can result from a variety of issues. For ideas on how
+to track down issues with unexpected lost atoms, see :ref:`Fast moving
+atoms <hint05>` and :ref:`Neighbor list settings <hint09>` in the
+general troubleshooting section above. In specific situations however,
+losing atoms is expected material behavior (e.g. with sputtering and
+surface evaporation simulations) and an unwanted crash can be resolved
+by changing the :doc:`thermo_modify lost <thermo_modify>` keyword from
+the default 'error' to 'warn' or 'ignore' (though heed the advice in
+:ref:`Ignoring lost atoms <hint06>` above!).
+
 .. _err0009:
 
 Too many neighbor bins
@@ -287,9 +410,88 @@ Too many neighbor bins
 The simulation box has become too large relative to the size of a
 neighbor bin and LAMMPS is unable to store the needed number of
 bins. This typically implies the simulation box has expanded too far.
-This can happen when some atoms move rapidly apart with shrink-wrap
+This can happen when some atoms move rapidly apart with shrink-wrap boundaries
-boundaries or when a fix (like fix deform or a barostat) excessively
+or when a fix (like fix deform or a barostat) excessively grows the simulation
-grows the simulation box.
+box.
+
+.. _err0010:
+
+Unrecognized pair style ... is part of ... package which is not enabled in this LAMMPS binary
+---------------------------------------------------------------------------------------------
+
+The LAMMPS executable (binary) being used was not compiled with a package
+containing the specified pair style. This indicates that the executable needs to
+be re-built after enabling the correct package in the relevant Makefile or CMake
+build directory. See :doc:`Section 3. Build LAMMPS <Build>` for more details.
+One can check if the expected package and pair style is present in the
+executable by running it with the ``-help`` (or ``-h``) flag on the command
+line. One common oversight, especially for beginner LAMMPS users, is to enable
+the package, but to forget to run commands to rebuild (e.g., to run the final
+``make`` or ``cmake`` command).
+
+If this error is occurring with an executable that the user does not control
+(e.g., through a module on HPC clusters), the user will need to get in contact
+with the relevant person or people who can update the executable.
+
+.. _err0012:
+
+fmt::format_error
+-----------------
+
+LAMMPS uses the `{fmt} library <https://fmt.dev>`_ for advanced string
+formatting tasks.  This is similar to the ``printf()`` family of
+functions from the standard C library, but more flexible.  If there is a
+bug in the LAMMPS code and the format string does not match the list of
+arguments or has some other error, this error message will be shown.
+You should contact the LAMMPS developers and report the bug as a `GitHub
+Bug Report Issue <https://github.com/lammps/lammps/issues>`_ along with
+sufficient information to easily reproduce it.
+
+
+.. _err0013:
+
+Substitution for illegal variable
+---------------------------------
+
+A variable in an input script or a variable expression was not found in
+the list of valid variables.  The most common reason for this is a typo
+somewhere in the input file such that the expression uses an invalid variable
+name.  The second most common reason is omitting the curly braces for a
+direct variable with a name that is not a single letter.  For example:
+
+.. code-block:: LAMMPS
+
+   variable cutoff index 10.0
+   pair_style lj/cut ${cutoff}  # this is correct
+   pair_style lj/cut $cutoff    # this is incorrect, LAMMPS looks for 'c' instead of 'cutoff'
+   variable c      index 5.0    # if $c is defined, LAMMPS subsitutes only '$c' and reads: 5utoff
+
+Another potential source of this error may be invalid command line
+variables (-var or -v argument) used when launching LAMMPS from an
+interactive shell or shell scripts.  An uncommon source for this error
+is using the :doc:`next command <next>` to advance through a list of values
+provided by an index style variable.  If there is no remaining element in
+the list, LAMMPS will delete the variable and any following expansion or
+reference attempt will trigger the error.
+
+Users with harder-to-track variable errors might also find reading
+:doc:`Section 5.2. Parsing rules for input scripts<Commands_parse>`
+helpful.
+
+.. _err0014:
+
+Bond atom missing in image check or box size check
+--------------------------------------------------
+
+This can be either an error or a warning depending on your
+:doc:`thermo_modify settings <thermo_modify>`.  It is flagged in a part
+of the LAMMPS code where it updates the domain decomposition and before
+it builds the neighbor lists.  It checks that both atoms of a bond are
+within the communication cutoff of a subdomain.  It is usually caused by
+atoms moving too fast (see the :ref:`paragraph on fast moving atoms
+<hint05>`), or by the :doc:`communication cutoff being too
+small <comm_modify>`, or by waiting too long between :doc:`sub-domain
+and neighbor list updates <neigh_modify>`.
 
 .. _err0015:
 
@@ -305,31 +507,211 @@ fill space. This error can be avoided using the generally slower
 :doc:`nsq neighbor style <neighbor>` or by increasing the size of the
 smallest box lengths.
 
+.. _err0016:
+
+Did not assign all atoms correctly
+----------------------------------
+
+This error happens most commonly when :doc:`reading a data file <read_data>`
+under :doc:`non-periodic boundary conditions<boundary>`.  Only atoms with
+positions **inside** the simulation box will be read and thus any atoms
+outside the box will be skipped and the total atom count will not match,
+which triggers the error.  This does not happen with periodic boundary
+conditions where atoms outside the principal box will be "wrapped" into
+the principal box and their image flags set accordingly.
+
+Similar errors can happen with the :doc:`replicate command<replicate>` or
+the :doc:`read_restart command<read_restart>`.  In these cases the cause
+may be a problematic geometry, an insufficient communication cutoff, or
+a bug in the LAMMPS source code.  In these cases it is advisable to set
+up :ref:`small test case <hint01>` for testing and debugging.  This will
+be required in case you need to get help from a LAMMPS developer.
+
 .. _err0017:
 
 Domain too large for neighbor bins
 ----------------------------------
 
 The domain has become extremely large so that neighbor bins cannot
-be used. Too many neighbor bins would need to be created to fill space
+be used. Too many neighbor bins would need to be created to fill space.
-Most likely, one or more atoms have been blown out of the simulation
+Most likely, one or more atoms have been blown a great distance out of
-box to a great distance or a fix (like fix deform or a barostat) has
+the simulation box or a fix (like fix deform or a barostat) has
 excessively grown the simulation box.
 
+.. _err0018:
+
+Step X: (h)bondchk failed
+-------------------------
+
+This error is a consequence of the heuristic memory allocations for
+buffers of the regular ReaxFF version.  In ReaxFF simulations, the lists
+of bonds and hydrogen bonds can change due to chemical reactions.  The
+default approach, however, assumes that these changes are not very
+large, so it allocates buffers for the current system setup plus a
+safety margin.  This can be adjusted with the :doc:`safezone, mincap,
+and minhbonds settings of the pair style <pair_reaxff>`, but only to some
+extent.  When equilibrating a new system, or simulating a sparse system
+in parallel, this can be difficult to control and become wasteful.  A
+simple workaround is often to break a simulation down in multiple
+chunks.  A better approach, however, is to compile and use the KOKKOS
+package version of ReaxFF (you do not need a GPU for that, but can also
+compile it in serial or OpenMP mode), which uses a more robust
+memory allocation approach.
+
+.. _err0019:
+
+Numeric index X is out of bounds
+--------------------------------
+
+This error most commonly happens when setting force field coefficients
+with either the :doc:`pair_coeff <pair_coeff>`, the :doc:`bond_coeff
+<bond_coeff>`, the :doc:`angle_coeff <angle_coeff>`, the
+:doc:`dihedral_coeff <dihedral_coeff>`, or the :doc:`improper_coeff
+<improper_coeff>` command.  These commands accept type labels,
+explicit numbers, and wildcards for ranges of numbers.  If the numeric
+value of any of these is outside the valid range (defined by the number
+of corresponding types), LAMMPS will stop with this error.  A few other
+commands and styles also allow ranges of numbers and check
+using the same method and thus print the same kind of error.
+
+The cause is almost always a typo in the input or a logic error
+when defining the values or ranges.  So one needs to carefully
+review the input.  Along with the error, LAMMPS will print the
+valid range as a hint.
+
+.. _err0020:
+
+Compute, fix, or variable vector or array is accessed out-of-range
+------------------------------------------------------------------
+
+When accessing an individual element of a global vector or array or a
+per-atom vector or array provided by a compute or fix or atom-style or
+vector-style variable or data from a specific atom, an index in square
+brackets ("[ ]") (or two indices) must be provided to determine which
+element to access and it must be in a valid range or else LAMMPS would
+access invalid data or crash with a segmentation fault. In the two most
+common cases, where this data is accessed, :doc:`variable expressions
+<variable>` and :doc:`thermodynamic output <thermo_style>`, LAMMPS will
+check for valid indices and stop with an error otherwise.
+
+While LAMMPS is written in C++ (which uses 0 based indexing) these
+indices start at 1 (i.e. similar to Fortran).  Any index smaller than 1
+or larger than the maximum allowed value should trigger this error.
+Since this kind of error frequently happens with rather complex
+expressions, it is recommended to test these with small test systems,
+where the values can be tracked with output files for all relevant
+properties at every step.
+
+.. _err0021:
+
+Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients)
+-------------------------------------------------------------------------------------
+
+The parameters in the :doc:`pair_coeff <pair_coeff>` command for a specified
+:doc:`pair_style <pair_style>` have a missing or erroneous argument. The same
+applies when seeing this error for :doc:`bond_coeff <bond_coeff>`,
+:doc:`angle_coeff <angle_coeff>`,  :doc:`dihedral_coeff <dihedral_coeff>`, or
+:doc:`improper_coeff <improper_coeff>` and their respective style commands when
+using the MOLECULE or EXTRA-MOLECULE packages. The cases below describe
+some ways to approach pair coefficient errors, but the same strategies
+apply to bonded systems as well.
+
+Outside of normal typos, this error can have several sources. In all cases, the
+first step is to compare the command arguments to the expected format found in
+the corresponding :doc:`pair_style <pair_style>` page. This can reveal cases
+where, for example, a pair style was changed, but the pair coefficients were not
+updated. This can happen especially with pair style variants such as
+:doc:`pair_style eam <pair_eam>` vs. :doc:`pair_style eam/alloy <pair_style>`
+that look very similar but accept different parameters (the latter 'eam/alloy'
+variant takes element type names while 'eam' does not).
+
+Another common source of coefficient errors is when using multiple pair styles
+with commands such as :doc:`pair_style hybrid <pair_hybrid>`. Using hybrid pair
+styles requires adding an extra "label" argument in the coefficient commands
+that designates which pair style the command line refers to. Moreover, if
+the same pair style is used multiple times, this label must be followed by
+an additional numeric argument. Also, different pair styles may require
+different arguments.
+
+This error message might also require a close look at other LAMMPS input files
+that are read in by the input script, such as data files or restart files.
+
+.. _err0022:
+
+Energy was not tallied on needed timestep (also virial, per-atom energy, per-atom virial)
+-----------------------------------------------------------------------------------------
+
+This error is generated when LAMMPS attempts to access an out-of-date or
+non-existent energy, pressure, or virial.  For efficiency reasons,
+LAMMPS does *not* calculate these quantities when the forces are
+calculated on every timestep or iteration.  Global quantities are only
+calculated when they are needed for :doc:`thermo <thermo_style>` output
+(at the beginning, end, and at regular intervals specified by the
+:doc:`thermo <thermo>` command). Similarly, per-atom quantities are only
+calculated if they are needed to write per-atom energy or virial to a
+dump file.  This system works fine for simple input scripts.  However,
+the many user-specified `variable`, `fix`, and `compute` commands that
+LAMMPS provides make it difficult to anticipate when a quantity will be
+requested. In some use cases, LAMMPS will figure out that a quantity is
+needed and arrange for it to be calculated on that timestep e.g. if it
+is requested by :doc:`fix ave/time <fix_ave_time>` or similar commands.
+If that fails, it can be detected by a mismatch between the current
+timestep and when a quantity was last calculated, in which case an error
+message of this type is generated.
+
+The most common cause of this type of error is requesting a quantity before
+the start of the simulation.
+
+.. code-block:: LAMMPS
+
+   # run 0 post no               # this will fix the error
+   variable e equal pe           # requesting energy compute
+   print "Potential energy = $e" # this will generate the error
+   run 1000                      # start of simulation
+
+This situation can be avoided by adding in a "run 0" command, as explained in
+more detail in the "Variable Accuracy" section of the
+:doc:`variable <variable>` doc page.
+
+Another cause is requesting a quantity on a timestep that is not
+a thermo or dump output timestep. This can often be
+remedied by increasing the frequency of thermo or dump output.
+
+.. _err0023:
+
+Molecule auto special bond generation overflow
+----------------------------------------------
+
+In order to correctly apply the :doc:`special_bonds <special_bonds>`
+settings (also known as "exclusions"), LAMMPS needs to maintain for each
+atom a list of atoms that are connected to this atom, either directly with
+a bond or indirectly through bonding with an intermediate atom(s). The purpose
+is to either remove or tag those pairs of atoms in the neighbor list.  This
+information is stored with individual
+atoms and thus the maximum number of such "special" neighbors is set
+when the simulation box is created.  When reading (relative) geometry
+and topology of a 'molecule' from a :doc:`molecule file <molecule>`,
+LAMMPS will build the list of such "special" neighbors for the molecule atom
+(if not given in the molecule file explicitly).  The error is triggered
+when the resulting list is too long for the space reserved when
+creating the simulation box.  The solution is to increase the
+corresponding setting.  Overestimating this value will only consume
+more memory, and is thus a safe choice.
+
 .. _err0024:
 
 Molecule topology/atom exceeds system topology/atom
 ---------------------------------------------------
 
 LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to
-distribute data (i.e. atoms) across the MPI processes in parallel runs.
+distribute data (i.e. atoms) across the MPI processes in parallel
-This includes topology data, that is data about bonds, angles,
+runs. This includes topology data about bonds, angles,
 dihedrals, impropers and :doc:`"special" neighbors <special_bonds>`.
 This information is stored with either one or all atoms involved in such
 a topology entry (which of the two option applies depends on the
-:doc:`newton <newton>` setting for bonds. When reading a data file,
+:doc:`newton <newton>` setting for bonds). When reading a data file,
-LAMMPS analyzes the requirements for this file and then the values
+LAMMPS analyzes the requirements for this file and then the values are
-are "locked in" and cannot be extended.
+"locked in" and cannot be extended.
 
 So loading a molecule file that requires more of the topology per atom
 storage or adding a data file with such needs will lead to an error.  To
@@ -367,3 +749,113 @@ example, are usually not a per-atom property, but defined through the
 atom type.  Thus it would not be required to have a Masses section and
 the included data would be ignored.  LAMMPS prints this warning to
 inform about this case.
+
+.. _err0027:
+
+Inconsistent image flags
+------------------------
+
+This warning happens when the distance between the *unwrapped* x-, y-,
+or z-components of the coordinates of a bond is larger than half the box
+with periodic boundaries or larger than the box with non-periodic
+boundaries.  It means that the positions and image flags have become
+inconsistent.  LAMMPS will still compute bonded interactions based on
+the closest periodic images of the atoms and thus in most cases the
+results will be correct.  Nevertheless, it is good practice to update
+the system so that the message does not appear.  It will help with
+future manipulations of the system.
+
+There is one case where this warning *must* appear: when you have a
+chain of connected bonds that pass through the entire box and connect
+back to the first atom in the chain through periodic boundaries,
+i.e. some kind of "infinite polymer".  In that case, the bond image
+flags *must* be inconsistent for the one bond that reaches back to the
+beginning of the chain.
+
+
+.. _err0028:
+
+No fixes with time integration, atoms won't move
+------------------------------------------------
+
+This warning will be issued if LAMMPS encounters a :doc:`run <run>` command that
+does not have a preceding :doc:`fix <fix>` command that updates atom/object
+positions and velocities per step. In other words, there are no fixes detected
+that perform velocity-Verlet time integration, such as :doc:`fix nve <fix_nve>`.
+Note that this alert does not mean that there are no active fixes. LAMMPS has a
+very wide variety of fixes, many of which do not move objects but also operate
+through steps, such as printing outputs (e.g. :doc:`fix print <fix_print>`),
+performing calculations (e.g. :doc:`fix ave/time <fix_ave_time>`), or changing
+other system parameters (e.g. :doc:`fix dt/reset <fix_dt_reset>`). It is up to
+the user to determine whether the lack of a time-integrating fix is intentional
+or not.
+
+
+.. _err0029:
+
+System is not charge neutral, net charge = ...
+----------------------------------------------
+
+the sum of charges in the system is not zero. When a system is not
+charge-neutral, methods that evolve/manipulate per-atom charges, evaluate
+Coulomb interactions, evaluate Coulomb forces, or evaluate/manipulate other
+properties relying on per-atom charges may raise this warning. A non-zero
+net charge most commonly arises after setting per-atom charges :doc:`set <set>`
+such that the sum is non-zero or by reading in a system through :doc:`read_data
+<read_data>` where the per-atom charges do not sum to zero. However, a loss of
+charge neutrality may occur in other less common ways, like when charge
+equilibration methods (e.g., :doc:`fix qeq <fix_qeq>`) fail.
+
+A similar warning/error may be raised when using certain charge equilibration
+methods: :doc:`fix qeq <fix_qeq>`, :doc:`fix qeq/comb <fix_qeq_comb>`, :doc:`fix
+qeq/reaxff <fix_qeq_reaxff>`, and :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`. In
+such cases, this warning/error will be raised for the fix :doc:`group <group>`
+when the group has a non-zero net charge.
+
+When the system is expected to be charge-neutral, this warning often arises due
+to an error in the lammps input (e.g., an incorrect :doc:`set <set>` command,
+error in the data file read by :doc:`read_data <read_data>`, incorrectly
+grouping atoms with charge, etc.). If the system is NOT expected to be
+charge-neutral, the user should make sure that the method(s) used are
+appropriate for systems with a non-zero net charge. Some commonly used fixes for
+charge equilibration :doc:`fix qeq <fix_qeq>`, pair styles that include charge
+interactions :doc:`pair_style coul/XXX <pair_coul>`, and kspace methods
+:doc:`kspace_style <kspace_style>` can, in theory, support systems with non-zero
+net charge. However, non-zero net charge can lead to spurious artifacts. The
+severity of these artifacts depends on the magnitude of total charge, system
+size, and methods used. Before running simulations or calculations for systems
+with non-zero net charge, users should test for artifacts and convergence of
+properties.
+
+.. _err0030:
+
+Variable evaluation before simulation box is defined
+----------------------------------------------------
+
+This error happens, when trying to expand or use an equal- or atom-style
+variable (or an equivalent style), where the expression contains a
+reference to something (e.g. a compute reference, a property of an atom,
+or a thermo keyword) that is not allowed to be used before the
+simulation box is defined.  See the paragraph on :ref:`errors before or
+after the simulation box is created <hint12>` for additional
+information.
+
+.. _err0031:
+
+Invalid thermo keyword 'X' in variable formula
+----------------------------------------------
+
+This error message is often misleading.  It is caused when evaluating a
+:doc:`variable command <variable>` expression and LAMMPS comes across a
+string that it does not recognize.  LAMMPS first checks if a string is a
+reference to a compute, fix, custom property, or another variable by
+looking at the first 2-3 characters (and if it is, it checks whether the
+referenced item exists).  Next LAMMPS checks if the string matches one
+of the available functions or constants.  If that fails, LAMMPS will
+assume that this string is a :doc:`thermo keyword <thermo_style>` and
+let the code for printing thermodynamic output return the corresponding
+value.  However, if this fails too, since the string is not a thermo
+keyword, LAMMPS stops with the 'Invalid thermo keyword' error.  But it
+is also possible, that there is just a typo in the name of a valid
+variable function.  Thus it is recommended to check the failing variable
+expression very carefully.

doc/src/Howto_peri.rst

@@ -197,7 +197,7 @@ The LPS model has a force scalar state
 .. math::
 
    \underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} +
-   \alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)}
+   \alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)}
 
 with :math:`K` the bulk modulus and :math:`\alpha` related to the shear
 modulus :math:`G` as
@@ -242,14 +242,14 @@ scalar state are defined, respectively, as
 
 .. math::
 
-   \underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad
+   \underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad
-   \underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i},
+   \underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i},
 
 
 where the arguments of the state functions and the vectors on which they
 operate are omitted for simplicity. We note that the LPS model is linear
 in the dilatation :math:`\theta`, and in the deviatoric part of the
-extension :math:`\underline{e}^{\rm d}`.
+extension :math:`\underline{e}^\mathrm{d}`.
 
 .. note::
 

doc/src/Howto_triclinic.rst

@@ -249,23 +249,23 @@ as follows:
 
 .. math::
 
-  a   = & {\rm lx} \\
+  a   = & \mathrm{lx} \\
-  b^2 = &  {\rm ly}^2 +  {\rm xy}^2 \\
+  b^2 = &  \mathrm{ly}^2 + \mathrm{xy}^2 \\
-  c^2 = &  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
+  c^2 = &  \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\
-  \cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
+  \cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\
-  \cos{\beta}  = & \frac{\rm xz}{c} \\
+  \cos{\beta}  = & \frac{\mathrm{xz}}{c} \\
-  \cos{\gamma} = & \frac{\rm xy}{b} \\
+  \cos{\gamma} = & \frac{\mathrm{xy}}{b} \\
 
 The inverse relationship can be written as follows:
 
 .. math::
 
-  {\rm lx}   = & a \\
+  \mathrm{lx}   = & a \\
-  {\rm xy}   = & b \cos{\gamma}  \\
+  \mathrm{xy}   = & b \cos{\gamma}  \\
-  {\rm xz}   = & c \cos{\beta}\\
+  \mathrm{xz}   = & c \cos{\beta}\\
-  {\rm ly}^2 = & b^2 - {\rm xy}^2 \\
+  \mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\
-  {\rm yz}   = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
+  \mathrm{yz}   = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\
-  {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
+  \mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\
 
 The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the

doc/src/Speed_compare.rst

@@ -44,11 +44,6 @@ section below for examples where this has been done.
   system the crossover (in single precision) is often about 50K-100K
   atoms per GPU.  When performing double precision calculations the
   crossover point can be significantly smaller.
-* Both KOKKOS and GPU package compute bonded interactions (bonds, angles,
-  etc) on the CPU.  If the GPU package is running with several MPI processes
-  assigned to one GPU, the cost of computing the bonded interactions is
-  spread across more CPUs and hence the GPU package can run faster in these
-  cases.
 * When using LAMMPS with multiple MPI ranks assigned to the same GPU, its
   performance depends to some extent on the available bandwidth between
   the CPUs and the GPU. This can differ significantly based on the
@@ -85,10 +80,10 @@ section below for examples where this has been done.
   code (with a performance penalty due to having data transfers between
   host and GPU).
 * The GPU package requires neighbor lists to be built on the CPU when using
-  exclusion lists, or a triclinic simulation box.
+  hybrid pair styles, exclusion lists, or a triclinic simulation box.
-* The GPU package can be compiled for CUDA or OpenCL and thus supports
+* The GPU package can be compiled for CUDA, HIP, or OpenCL and thus supports
-  both, NVIDIA and AMD GPUs well. On NVIDIA hardware, using CUDA is typically
+  NVIDIA, AMD, and Intel GPUs well. On NVIDIA hardware, using CUDA is
-  resulting in equal or better performance over OpenCL.
+  typically resulting in equal or better performance over OpenCL.
 * OpenCL in the GPU package does theoretically also support Intel CPUs or
   Intel Xeon Phi, but the native support for those in KOKKOS (or INTEL)
   is superior.

doc/src/bond_bpm_spring.rst

@@ -142,7 +142,7 @@ is accordingly replaced with a square root. This approximation assumes bonds
 are evenly distributed on a spherical surface and neglects constant prefactors
 which are irrelevant since only the ratio of volumes matters. This term may be
 used to adjust the Poisson's ratio. See the simulation in the
-examples/bpm/poissons_ratio directory for a demonstration of this effect.
+``examples/bpm/poissons_ratio`` directory for a demonstration of this effect.
 
 If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
 (or adding) that bond's contribution.
@@ -153,7 +153,7 @@ the data file or restart files read by the :doc:`read_data
 <read_data>` or :doc:`read_restart <read_restart>` commands:
 
 * :math:`k`             (force/distance units)
-* :math:`\epsilon_c`    (unit less)
+* :math:`\epsilon_c`    (unitless)
 * :math:`\gamma`        (force/velocity units)
 
 Additionally, if *volume/factor* is set to *yes*, a fourth coefficient

doc/src/bond_bpm_spring_plastic.rst

@@ -108,9 +108,9 @@ the data file or restart files read by the :doc:`read_data
 <read_data>` or :doc:`read_restart <read_restart>` commands:
 
 * :math:`k`             (force/distance units)
-* :math:`\epsilon_c`    (unit less)
+* :math:`\epsilon_c`    (unitless)
 * :math:`\gamma`        (force/velocity units)
-* :math:`\epsilon_p     (unit less)
+* :math:`\epsilon_p`    (unitless)
 
 See the :doc:`bpm/spring doc page <bond_bpm_spring>` for information on
 the *smooth*, *normalize*, *break*, *overlay/pair*, and *store/local*
@@ -133,16 +133,17 @@ Restart and other info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 This bond style writes the reference state and plastic history of each
-bond to :doc:`binary restart files <restart>`. Loading a restart
+bond to :doc:`binary restart files <restart>`. Loading a restart file
-file will properly restore bonds. However, the reference state is NOT
+will properly restore bonds. However, the reference state is NOT written
-written to data files. Therefore reading a data file will not
+to data files.  Therefore reading a data file will not restore bonds and
-restore bonds and will cause their reference states to be redefined.
+will cause their reference states to be redefined.
 
-The potential energy and the single() function of this bond style returns zero.
+The potential energy and the single() function of this bond style
-The single() function also calculates two extra bond quantities, the initial
+returns zero.  The single() function also calculates two extra bond
-distance :math:`r_0` and the current equilbrium length :math:`r_eq`. These extra
+quantities, the initial distance :math:`r_0` and the current equilibrium
-quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
+length :math:`r_eq`. These extra quantities can be accessed by the
-command as *b1* and *b2*, respectively.
+:doc:`compute bond/local <compute_bond_local>` command as *b1* and *b2*,
+respectively.
 
 Restrictions
 """"""""""""

doc/src/bond_harmonic.rst

@@ -60,6 +60,8 @@ Related commands
 """"""""""""""""
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
+:doc:`bond style harmonic/shift <bond_harmonic_shift>`,
+:doc:`bond style harmonic/shift/cut <bond_harmonic_shift_cut>`
 
 Default
 """""""

doc/src/bond_harmonic_shift.rst

@@ -31,9 +31,15 @@ the potential
 
    E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
 
-where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
+where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the
-The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
+critical distance.  The potential energy has the value
-:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
+:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`.  This
+bond style differs from :doc:`bond_style harmonic <bond_harmonic>`
+by the value of the potential energy.
+
+The equivalent spring constant value *K* for use with :doc:`bond_style
+harmonic <bond_harmonic>` can be computed using :math:`K =
+U_{\text{min}} / [(r_0-r_c)^2]`.
 
 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in
@@ -41,9 +47,7 @@ the data file or restart files read by the :doc:`read_data <read_data>`
 or :doc:`read_restart <read_restart>` commands:
 
 * :math:`U_{\text{min}}` (energy)
-
 * :math:`r_0` (distance)
-
 * :math:`r_c` (distance)
 
 ----------
@@ -63,7 +67,8 @@ Related commands
 """"""""""""""""
 
 :doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
-:doc:`bond_harmonic <bond_harmonic>`
+:doc:`bond style harmonic <bond_harmonic>`,
+:doc:`bond style harmonic/shift/cut <bond_harmonic_shift_cut>`
 
 Default
 """""""

doc/src/bond_harmonic_shift_cut.rst

@@ -31,9 +31,14 @@ uses the potential
 
    E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
 
-where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
+where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the
-The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
+critical distance.  The bond potential is zero and thus its force also
-at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
+zero for distances :math:`r > r_c`.  The potential energy has the value
+:math:`-U_{\text{min}}` at :math:`r_0` and zero at :math:`r_c`.
+
+The equivalent spring constant value *K* for use with :doc:`bond_style
+harmonic <bond_harmonic>` for :math:`r <= r_c`, can be computed using
+:math:`K = U_{\text{min}} / [(r_0-r_c)^2]`
 
 The following coefficients must be defined for each bond type via the
 :doc:`bond_coeff <bond_coeff>` command as in the example above, or in

doc/src/bond_rheo_shell.rst

@@ -94,7 +94,7 @@ the data file or restart files read by the :doc:`read_data
 <read_data>` or :doc:`read_restart <read_restart>` commands:
 
 * :math:`k`             (force/distance units)
-* :math:`\epsilon_c`    (unit less)
+* :math:`\epsilon_c`    (unitless)
 * :math:`\gamma`        (force/velocity units)
 
 Unlike other BPM-style bonds, this bond style does not update special

doc/src/compute_cna_atom.rst

@@ -67,7 +67,7 @@ following relation should also be satisfied:
 
 .. math::
 
-  r_c + r_s > 2*{\rm cutoff}
+  r_c + r_s > 2*\mathrm{cutoff}
 
 where :math:`r_c` is the cutoff distance of the potential, :math:`r_s`
 is the skin

doc/src/compute_cnp_atom.rst

@@ -74,7 +74,7 @@ following relation should also be satisfied:
 
 .. math::
 
-  r_c + r_s > 2*{\rm cutoff}
+  r_c + r_s > 2*\mathrm{cutoff}
 
 where :math:`r_c` is the cutoff distance of the potential, :math:`r_s` is
 the skin

doc/src/compute_efield_wolf_atom.rst

@@ -50,9 +50,9 @@ the potential energy using the Wolf summation method, described in
 
 .. math::
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
 are error-function and complementary error-function terms.  This

doc/src/compute_hexorder_atom.rst

@@ -40,7 +40,7 @@ is a complex number (stored as two real numbers) defined as follows:
 
 .. math::
 
-   q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\bf r}_{ij})}
+   q_n = \frac{1}{nnn}\sum_{j = 1}^{nnn} e^{n i \theta({\textbf{r}}_{ij})}
 
 where the sum is over the *nnn* nearest neighbors
 of the central atom. The angle :math:`\theta`

doc/src/compute_orientorder_atom.rst

@@ -49,7 +49,7 @@ For each atom, :math:`Q_\ell` is a real number defined as follows:
 
 .. math::
 
-   \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) \bigr) \\
+   \bar{Y}_{\ell m} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{\ell m}\bigl( \theta( \mathbf{r}_{ij} ), \phi( \mathbf{r}_{ij} ) \bigr) \\
    Q_\ell  = & \sqrt{\frac{4 \pi}{2 \ell  + 1} \sum_{m = -\ell }^{m = \ell } \bar{Y}_{\ell m} \bar{Y}^*_{\ell m}}
 
 The first equation defines the local order parameters as averages

doc/src/compute_sna_atom.rst

@@ -139,11 +139,11 @@ mapped on to a third polar angle :math:`\theta_0` defined by,
 
 .. math::
 
-  \theta_0 = {\sf rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
+  \theta_0 = \mathsf{rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
 
 In this way, all possible neighbor positions are mapped on to a subset
-of the 3-sphere.  Points south of the latitude :math:`\theta_0` =
+of the 3-sphere.  Points south of the latitude
-*rfac0* :math:`\pi` are excluded.
+:math:`\theta_0 = \mathsf{rfac0} \pi` are excluded.
 
 The natural basis for functions on the 3-sphere is formed by the
 representatives of *SU(2)*, the matrices :math:`U^j_{m,m'}(\theta, \phi,
@@ -204,7 +204,7 @@ components summed separately for each LAMMPS atom type:
 
 .. math::
 
-   -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial {\bf r}_i}
+   -\sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial \mathbf{r}_i}
 
 The sum is over all atoms *i'* of atom type *I*\ .  For each atom *i*,
 this compute evaluates the above expression for each direction, each
@@ -216,7 +216,7 @@ derivatives:
 
 .. math::
 
-  -{\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
+  -\mathbf{r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial \mathbf{r}_i}
 
 Again, the sum is over all atoms *i'* of atom type *I*\ .  For each atom
 *i*, this compute evaluates the above expression for each of the six

doc/src/compute_stress_atom.rst

@@ -65,7 +65,7 @@ In case of compute *stress/atom*, the virial contribution is:
 
    W_{ab} & = \frac{1}{2} \sum_{n = 1}^{N_p} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b}) + \frac{1}{2} \sum_{n = 1}^{N_b} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b})  \\
   & + \frac{1}{3} \sum_{n = 1}^{N_a} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b}) + \frac{1}{4} \sum_{n = 1}^{N_d} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) \\
-  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+  & + \frac{1}{4} \sum_{n = 1}^{N_i} (r_{1_a} F_{1_b} + r_{2_a} F_{2_b} + r_{3_a} F_{3_b} + r_{4_a} F_{4_b}) + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
 The first term is a pairwise energy contribution where :math:`n` loops
 over the :math:`N_p` neighbors of atom :math:`I`, :math:`\mathbf{r}_1`
@@ -97,7 +97,7 @@ In case of compute *centroid/stress/atom*, the virial contribution is:
 .. math::
 
    W_{ab} & = \sum_{n = 1}^{N_p} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_b} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_a} r_{I0_a}  F_{I_b} + \sum_{n = 1}^{N_d} r_{I0_a} F_{I_b} + \sum_{n = 1}^{N_i} r_{I0_a} F_{I_b} \\
-  & + {\rm Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
+  & + \mathrm{Kspace}(r_{i_a},F_{i_b}) + \sum_{n = 1}^{N_f} r_{i_a} F_{i_b}
 
 As with compute *stress/atom*, the first, second, third, fourth and
 fifth terms are pairwise, bond, angle, dihedral and improper

doc/src/fitpod_command.rst

@@ -263,10 +263,10 @@ then the globally defined weights from the ``fitting_weight_energy`` and
 POD Potential
 """""""""""""
 
-We consider a multi-element system of *N* atoms with :math:`N_{\rm e}`
+We consider a multi-element system of *N* atoms with :math:`N_\mathrm{e}`
 unique elements.  We denote by :math:`\boldsymbol r_n` and :math:`Z_n`
 position vector and type of an atom *n* in the system,
-respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_{\rm e}
+respectively. Note that we have :math:`Z_n \in \{1, \ldots, N_\mathrm{e}
 \}`, :math:`\boldsymbol R = (\boldsymbol r_1, \boldsymbol r_2, \ldots,
 \boldsymbol r_N) \in \mathbb{R}^{3N}`, and :math:`\boldsymbol Z = (Z_1,
 Z_2, \ldots, Z_N) \in \mathbb{N}^{N}`. The total energy of the

doc/src/fix.rst

@@ -341,8 +341,8 @@ accelerated styles exist.
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
 * :doc:`pimd/langevin <fix_pimd>` - Feynman path-integral molecular dynamics with stochastic thermostat
 * :doc:`pimd/nvt <fix_pimd>` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat
-* :doc:`pimd/langevin/bosonic <fix_pimd_bosonic>` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat
+* :doc:`pimd/langevin/bosonic <fix_pimd>` - Bosonic Feynman path-integral molecular dynamics for with stochastic thermostat
-* :doc:`pimd/nvt/bosonic <fix_pimd_bosonic>` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat
+* :doc:`pimd/nvt/bosonic <fix_pimd>` - Bosonic Feynman path-integral molecular dynamics with Nose-Hoover thermostat
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
 * :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
 * :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies

doc/src/fix_adapt.rst

@@ -236,6 +236,8 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`wf/cut <pair_wf_cut>`                                                  | epsilon,sigma,nu,mu                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`yukawa <pair_yukawa>`                                                  | alpha                                            | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 
 .. note::
 

doc/src/fix_ave_chunk.rst

@@ -459,8 +459,8 @@ output.  This option can only be used with the *ave running* setting.
 
 The *format* keyword sets the numeric format of each value when it is
 printed to a file via the *file* keyword.  Note that all values are
-floating point quantities.  The default format is %g.  You can specify
+floating point quantities.  The default format is " %g".  You can specify
-a higher precision if desired (e.g., %20.16g).
+a higher precision if desired (e.g., " %20.16g").
 
 The *title1* and *title2* and *title3* keywords allow specification of
 the strings that will be printed as the first three lines of the output

doc/src/fix_ave_time.rst

@@ -304,8 +304,8 @@ output.  This option can only be used with the *ave running* setting.
 
 The *format* keyword sets the numeric format of each value when it is
 printed to a file via the *file* keyword.  Note that all values are
-floating point quantities.  The default format is %g.  You can specify
+floating point quantities.  The default format is " %g".  You can specify
-a higher precision if desired (e.g., %20.16g).
+a higher precision if desired (e.g., " %20.16g").
 
 The *title1* and *title2* and *title3* keywords allow specification of
 the strings that will be printed as the first 2 or 3 lines of the

doc/src/fix_gld.rst

@@ -60,9 +60,9 @@ With this fix active, the force on the *j*\ th atom is given as
 
 .. math::
 
-   {\bf F}_{j}(t) = & {\bf F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) {\bf v}_j(s)~\text{d}s + {\bf F}^R_j(t) \\
+   \mathbf{F}_{j}(t) = & \mathbf{F}^C_j(t)-\int \limits_{0}^{t} \Gamma_j(t-s) \mathbf{v}_j(s)~\text{d}s + \mathbf{F}^R_j(t) \\
    \Gamma_j(t-s) = & \sum \limits_{k=1}^{N_k} \frac{c_k}{\tau_k} e^{-(t-s)/\tau_k} \\
-   \langle{\bf F}^R_j(t),{\bf F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s)
+   \langle\mathbf{F}^R_j(t),\mathbf{F}^R_j(s)\rangle = & \text{k$_\text{B}$T} ~\Gamma_j(t-s)
 
 Here, the first term is representative of all conservative (pairwise,
 bonded, etc) forces external to this fix, the second is the temporally

doc/src/fix_halt.rst

@@ -25,13 +25,14 @@ Syntax
 * operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
 * avalue = numeric value to compare attribute to
 * zero or more keyword/value pairs may be appended
-* keyword = *error* or *message* or *path*
+* keyword = *error* or *message* or *path* or *universe*
 
   .. parsed-literal::
 
        *error* value = *hard* or *soft* or *continue*
        *message* value = *yes* or *no*
        *path* value = path to check for free space (may be in quotes)
+       *universe* value = *yes* or *no*
 
 
 Examples
@@ -40,8 +41,10 @@ Examples
 .. code-block:: LAMMPS
 
    fix 10 all halt 1 bondmax > 1.5
-   fix 10 all halt 10 v_myCheck != 0 error soft
+   fix 10 all halt 10 v_myCheck != 0 error soft message no
    fix 10 all halt 100 diskfree < 100000.0 path "dump storage/."
+   fix  2 all halt 100 v_curtime > ${maxtime} universe yes
+
 
 Description
 """""""""""
@@ -141,33 +144,52 @@ The optional *error* keyword determines how the current run is halted.
 If its value is *hard*, then LAMMPS will stop with an error message.
 
 If its value is *soft*, LAMMPS will exit the current run, but continue
-to execute subsequent commands in the input script.  However,
+to execute subsequent commands in the input script.  However, additional
-additional :doc:`run <run>` or :doc:`minimize <minimize>` commands will be
+:doc:`run <run>` or :doc:`minimize <minimize>` commands will be skipped.
-skipped.  For example, this allows a script to output the current
+For example, this allows a script to output the current state of the
-state of the system, e.g. via a :doc:`write_dump <write_dump>` or
+system, e.g. via a :doc:`write_dump <write_dump>` or :doc:`write_restart
-:doc:`write_restart <write_restart>` command.
+<write_restart>` command.  To re-enable regular runs after *fix halt*
+stopped a run, you need to issue a :doc:`timer timeout unlimited
+<timer>` command.
 
 If its value is *continue*, the behavior is the same as for *soft*,
 except subsequent :doc:`run <run>` or :doc:`minimize <minimize>` commands
 are executed.  This allows your script to remedy the condition that
-triggered the halt, if necessary.  Note that you may wish use the
+triggered the halt, if necessary.  This is the equivalent of stopping
-:doc:`unfix <unfix>` command on the fix halt ID, so that the same
+with *error soft* and followed by :doc:`timer timeout unlimited
-condition is not immediately triggered in a subsequent run.
+<timer>` command.  This can have undesired consequences, when a
+:doc:`run command <run>` uses the *every* keyword, so using *error soft*
+and resetting the timer manually may be the preferred option.
+
+You may wish use the :doc:`unfix <unfix>` command on the *fix halt* ID
+before starting a subsequent run, so that the same condition is not
+immediately triggered again.
 
 The optional *message* keyword determines whether a message is printed
 to the screen and logfile when the halt condition is triggered.  If
 *message* is set to yes, a one line message with the values that
-triggered the halt is printed.  If *message* is set to no, no message
+triggered the halt is printed.  If *message* is set to no, no message is
-is printed; the run simply exits.  The latter may be desirable for
+printed; the run simply exits.  The latter may be desirable for
 post-processing tools that extract thermodynamic information from log
 files.
 
+.. versionadded:: TBD
+
+The optional *universe* keyword determines whether the halt request
+should be synchronized across the partitions of a :doc:`multi-partition
+run <Run_options>`.  If *universe* is set to yes, fix halt will check if
+there is a specific message received from any of the other partitions
+requesting to stop the run on this partition as well.  Consequently, if
+fix halt determines to halt the simulation, the fix will send messages
+to all other partitions so they stop their runs, too.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global or per-atom quantities are stored
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-by this fix for access by various :doc:`output commands <Howto_output>`.
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
@@ -183,4 +205,4 @@ Related commands
 Default
 """""""
 
-The option defaults are error = soft, message = yes, and path = ".".
+The option defaults are error = soft, message = yes, path = ".", and universe = no.

doc/src/fix_lb_fluid.rst

@@ -130,7 +130,7 @@ calculated as:
 
 .. math::
 
-   {\bf F}_{j \alpha} = \gamma \left({\bf v}_n - {\bf u}_f \right) \zeta_{j\alpha}
+   \mathbf{F}_{j \alpha} = \gamma \left(\mathbf{v}_n - \mathbf{u}_f \right) \zeta_{j\alpha}
 
 where :math:`\mathbf{v}_n` is the velocity of the MD particle,
 :math:`\mathbf{u}_f` is the fluid velocity interpolated to the particle

doc/src/fix_neb.rst

@@ -180,7 +180,7 @@ force is added.
 
 By default, no additional forces act on the first and last replicas
 during the NEB relaxation, so these replicas simply relax toward their
-respective local minima.  By using the key word *end*, additional forces
+respective local minima.  By using the keyword *end*, additional forces
 can be applied to the first and/or last replicas, to enable them to
 relax toward a MEP while constraining their energy E to the target
 energy ETarget.

doc/src/fix_nh.rst

@@ -208,19 +208,19 @@ The relaxation rate of the barostat is set by its inertia :math:`W`:
 
 .. math::
 
-   W = (N + 1) k_B T_{\rm target} P_{\rm damp}^2
+   W = (N + 1) k_B T_\mathrm{target} P_\mathrm{damp}^2
 
 where :math:`N` is the number of atoms, :math:`k_B` is the Boltzmann constant,
-and :math:`T_{\rm target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
+and :math:`T_\mathrm{target}` is the target temperature of the barostat :ref:`(Martyna) <nh-Martyna>`.
-If a thermostat is defined, :math:`T_{\rm target}` is the target temperature
+If a thermostat is defined, :math:`T_\mathrm{target}` is the target temperature
-of the thermostat. If a thermostat is not defined, :math:`T_{\rm target}`
+of the thermostat. If a thermostat is not defined, :math:`T_\mathrm{target}`
 is set to the current temperature of the system when the barostat is initialized.
 If this temperature is too low the simulation will quit with an error.
-Note: in previous versions of LAMMPS, :math:`T_{\rm target}` would default to
+Note: in previous versions of LAMMPS, :math:`T_\mathrm{target}` would default to
 a value of 1.0 for *lj* units and 300.0 otherwise if the system had a temperature
 of exactly zero.
 
-If a thermostat is not specified by this fix, :math:`T_{\rm target}` can be
+If a thermostat is not specified by this fix, :math:`T_\mathrm{target}` can be
 manually specified using the *Ptemp* parameter. This may be useful if the
 barostat is initialized when the current temperature does not reflect the
 steady state temperature of the system. This keyword may also be useful in
@@ -512,8 +512,8 @@ according to the following factorization of the Liouville propagator
 .. math::
 
    \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E}
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
    &\times \left[
@@ -526,8 +526,8 @@ according to the following factorization of the Liouville propagator
    &\times
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
    &+ \mathcal{O} \left(\Delta t^3 \right)
 
 This factorization differs somewhat from that of Tuckerman et al, in

doc/src/fix_npt_cauchy.rst

@@ -426,8 +426,8 @@ according to the following factorization of the Liouville propagator
 .. math::
 
    \exp \left(\mathrm{i} L \Delta t \right) = & \hat{E}
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right) \\
    &\times \left[
@@ -440,8 +440,8 @@ according to the following factorization of the Liouville propagator
    &\times
    \exp \left(\mathrm{i} L_{2}^{(2)} \frac{\Delta t}{2} \right)
    \exp \left(\mathrm{i} L_{\epsilon , 2} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}part} \frac{\Delta t}{2} \right)
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}part} \frac{\Delta t}{2} \right)
-   \exp \left(\mathrm{i} L_{\rm T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
+   \exp \left(\mathrm{i} L_\mathrm{T\textrm{-}baro} \frac{\Delta t}{2} \right) \\
    &+ \mathcal{O} \left(\Delta t^3 \right)
 
 This factorization differs somewhat from that of Tuckerman et al, in

doc/src/fix_orient.rst

@@ -62,19 +62,19 @@ The potential energy added to atom I is given by these formulas
 
 .. math::
 
-   \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(1\right) \\
+   \xi_{i} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(1\right) \\
    \\
-  \xi_{\rm IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^{\rm J} - \mathbf{r}_{j}^{\rm I} \right| \qquad\qquad\left(2\right)\\
+  \xi_\mathrm{IJ} = & \sum_{j=1}^{12} \left| \mathbf{r}_{j}^\mathrm{J} - \mathbf{r}_{j}^\mathrm{I} \right| \qquad\qquad\left(2\right)\\
   \\
-  \xi_{\rm low}  = & {\rm cutlo} \, \xi_{\rm IJ}  \qquad\qquad\qquad\left(3\right)\\
+  \xi_\mathrm{low}  = & \mathrm{cutlo} \, \xi_\mathrm{IJ}  \qquad\qquad\qquad\left(3\right)\\
-  \xi_{\rm high}  = & {\rm cuthi} \, \xi_{\rm IJ} \qquad\qquad\qquad\left(4\right) \\
+  \xi_\mathrm{high}  = & \mathrm{cuthi} \, \xi_\mathrm{IJ} \qquad\qquad\qquad\left(4\right) \\
   \\
-  \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_{\rm low}}{\xi_{\rm high} - \xi_{\rm low}} \qquad\qquad\left(5\right)\\
+  \omega_{i} = & \frac{\pi}{2} \frac{\xi_{i} - \xi_\mathrm{low}}{\xi_\mathrm{high} - \xi_\mathrm{low}} \qquad\qquad\left(5\right)\\
   \\
-  u_{i}  = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_{\rm low}\\
+  u_{i}  = & 0 \quad\quad\qquad\qquad\qquad \textrm{ for } \qquad \xi_{i} < \xi_\mathrm{low}\\
-         = & {\rm dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
+         = & \mathrm{dE}\,\frac{1 - \cos(2 \omega_{i})}{2}
-   \qquad \mathrm{ for }\qquad \xi_{\rm low} < \xi_{i} < \xi_{\rm high}  \quad \left(6\right) \\
+   \qquad \mathrm{for }\qquad \xi_\mathrm{low} < \xi_{i} < \xi_\mathrm{high}  \quad \left(6\right) \\
-         = & {\rm dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_{\rm high} < \xi_{i}
+         = & \mathrm{dE} \quad\qquad\qquad\qquad\textrm{ for } \qquad \xi_\mathrm{high} < \xi_{i}
 
 which are fully explained in :ref:`(Janssens) <Janssens>`.  For fcc crystals
 this order parameter Xi for atom I in equation (1) is a sum over the

doc/src/fix_pimd.rst

@@ -9,11 +9,11 @@ fix pimd/langevin command
 fix pimd/nvt command
 ====================
 
-:doc:`fix pimd/langevin/bosonic <fix_pimd_bosonic>` command
+fix pimd/langevin/bosonic command
-===========================================================
+=================================
 
-:doc:`fix pimd/nvt/bosonic <fix_pimd_bosonic>` command
+fix pimd/nvt/bosonic command
-======================================================
+============================
 
 Syntax
 """"""
@@ -23,7 +23,7 @@ Syntax
    fix ID group-ID style keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
+* style = *pimd/langevin* or *pimd/nvt* or *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command
 * zero or more keyword/value pairs may be appended
 * keywords for style *pimd/nvt*
 
@@ -89,19 +89,20 @@ partition function for the original system to a classical partition
 function for a ring-polymer system is exploited, to efficiently sample
 configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
 
-.. versionadded:: 11Mar2025
+.. versionadded:: TBD
 
    Fix *pimd/langevin/bosonic* and *pimd/nvt/bosonic* were added.
 
 Fix *pimd/nvt* and fix *pimd/langevin* simulate *distinguishable* quantum particles.
-Simulations of bosons, including exchange effects, are supported with the :doc:`fix pimd/langevin/bosonic <fix_pimd_bosonic>` and :doc:`fix pimd/nvt/bosonic <fix_pimd_bosonic>` commands.
+Simulations of bosons, including exchange effects, are supported with the
+fix *pimd/langevin/bosonic* and the *pimd/nvt/bosonic* commands.
 
 For distinguishable particles, the isomorphic classical partition function and its components are given
 by the following equations:
 
 .. math::
 
-   Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
+   Z = & \int d\mathbf{q} d\mathbf{p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
    H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\
    V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
@@ -173,15 +174,17 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
 
    Mode *pimd* added to fix pimd/langevin.
 
-Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default value is *nmpimd*.
+Fix pimd/langevin supports the *method* values *nmpimd* and *pimd*. The default
-If *method* is *nmpimd*, the normal mode representation is used to integrate the equations of motion.
+value is *nmpimd*.  If *method* is *nmpimd*, the normal mode representation is
-The exact solution of harmonic oscillator is used to propagate the free ring polymer part of the Hamiltonian.
+used to integrate the equations of motion.  The exact solution of harmonic
-If *method* is *pimd*, the Cartesian representation is used to integrate the equations of motion.
+oscillator is used to propagate the free ring polymer part of the Hamiltonian.
-The harmonic force is added to the total force of the system, and the numerical integrator is used to propagate the Hamiltonian.
+If *method* is *pimd*, the Cartesian representation is used to integrate the
+equations of motion.  The harmonic force is added to the total force of the
+system, and the numerical integrator is used to propagate the Hamiltonian.
 
-The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
+The keyword *integrator* specifies the Trotter splitting method used by *fix
-See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
+pimd/langevin*.  See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB
-either of the two should work fine.
+splitting schemes. Typically either of the two should work fine.
 
 The keyword *fmass* sets a further scaling factor for the fictitious
 masses of beads, which can be used for the Partial Adiabatic CMD
@@ -231,8 +234,8 @@ a positive floating-point number.
    For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference
    for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
 
-The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
+The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*.
-be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
+*style* can only be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
 
 .. note::
 
@@ -418,7 +421,12 @@ LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 Fix *pimd/nvt* cannot be used with :doc:`lj units <units>`.
-Fix *pimd/langevin* can be used with :doc:`lj units <units>`. See the above part for how to use it.
+Fix *pimd/langevin* can be used with :doc:`lj units <units>`.
+See the documentation above for how to use it.
+
+Only some combinations of fix styles and their options support
+partitions with multiple processors.  LAMMPS will stop with an
+error if multi-processor partitions are not supported.
 
 A PIMD simulation can be initialized with a single data file read via
 the :doc:`read_data <read_data>` command.  However, this means all
@@ -435,7 +443,7 @@ variable, e.g.
 Related commands
 """"""""""""""""
 
-:doc:`pimd/nvt/bosonic <fix_pimd_bosonic>`, :doc:`pimd/langevin/bosonic <fix_pimd_bosonic>`
+:doc:`fix ipi <fix_ipi>`
 
 Default
 """""""

doc/src/fix_pimd_bosonic.rst

@@ -1,237 +0,0 @@
-.. index:: fix pimd/langevin/bosonic
-.. index:: fix pimd/nvt/bosonic
-
-fix pimd/langevin/bosonic command
-=================================
-
-fix pimd/nvt/bosonic command
-============================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   fix ID group-ID style keyword value ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *pimd/langevin/bosonic* or *pimd/nvt/bosonic* = style name of this fix command
-* zero or more keyword/value pairs may be appended
-* keywords for style *pimd/nvt/bosonic*
-
-  .. parsed-literal::
-
-     *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
-     *method* value = *pimd* or *nmpimd*
-     *fmass* value = scaling factor on mass
-     *sp* value = scaling factor on Planck constant
-     *temp* value = temperature (temperature units)
-     *nhc* value = Nc = number of chains in Nose-Hoover thermostat
-
-* keywords for style *pimd/langevin/bosonic*
-
-  .. parsed-literal::
-
-     *keywords* = *integrator* or *ensemble* or *fmass* or *temp* or *thermostat* or *tau* or *fixcom* or *lj* or *esych*
-     *integrator* value = *obabo* or *baoab*
-     *ensemble* value = *nvt* or *nve*
-     *fmass* value = scaling factor on mass
-     *temp* value = temperature (temperature unit)
-          temperature = target temperature of the thermostat
-     *thermostat* values = style seed
-          style value = *PILE_L*
-          seed = random number generator seed
-     *tau* value = thermostat damping parameter (time unit)
-     *fixcom* value = *yes* or *no*
-     *lj* values = epsilon sigma mass planck mvv2e
-          epsilon = energy scale for reduced units (energy units)
-          sigma = length scale for reduced units (length units)
-          mass = mass scale for reduced units (mass units)
-          planck = Planck's constant for other unit style
-          mvv2e = mass * velocity^2 to energy conversion factor for other unit style
-     *esynch* value = *yes* or *no*
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all pimd/nvt/bosonic method pimd fmass 1.0 sp 1.0 temp 2.0 nhc 4
-   fix 1 all pimd/langevin/bosonic integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0
-
-Example input files are provided in the examples/PACKAGES/pimd_bosonic directory.
-
-Description
-"""""""""""
-
-These fix commands are based on the fixes :doc:`pimd/nvt and
-pimd/langevin <fix_pimd>` for performing quantum molecular dynamics
-simulations based on the Feynman path-integral formalism. The key
-difference is that fix *pimd/nvt* and fix *pimd/langevin* simulate
-*distinguishable* particles, while fix *pimd/nvt/bosonic* and fix
-*pimd/langevin/bosonic* perform simulations of bosons, including exchange
-effects. The *bosonic* commands share syntax with the equivalent commands for distinguishable particles.
-The user is referred to the documentation of :doc:`these commands <fix_pimd>`
-for a detailed syntax description and additional, general capabilities
-of the commands. The major differences from fix *pimd/nvt* and fix *pimd/langevin* in terms of
-capabilities are:
-
-* Fix *pimd/nvt/bosonic* only supports the "pimd" and "nmpimd" methods. Fix
-  *pimd/langevin/bosonic* only supports the "pimd" method, which is the default
-  in this fix. These restrictions are related to the use of normal
-  modes, which change in bosons. For similar reasons, *fmmode* of
-  *pimd/langevin* should not be used, and would raise an error if set to
-  a value other than *physical*.
-* Fix *pimd/langevin/bosonic* currently does not support *ensemble* other than
-  *nve*, *nvt*. The barostat related keywords *iso*, *aniso*,
-  *barostat*, *taup* are not supported.
-* Fix *pimd/langevin/bosonic* also has a keyword not available in fix
-  *pimd/langevin*: *esynch*, with default *yes*. If set to *no*, some
-  time consuming synchronization of spring energies and the primitive
-  kinetic energy estimator between processors is avoided.
-
-The isomorphism between the partition function of :math:`N` bosonic
-quantum particles and that of a system of classical ring polymers at
-inverse temperature :math:`\beta` is given by :ref:`(Tuckerman)
-<book-Tuckerman>`:
-
-.. math::
-
-   Z \propto \int d{\bf q} \cdot \frac{1}{N!} \sum_\sigma \textrm{exp} [ -\beta \left( E^\sigma + V \right) ].
-
-Here, :math:`V` is the potential between different particles at the same
-imaginary time slice, which is the same for bosons and distinguishable
-particles. The sum is over all permutations :math:`\sigma`. Recall that
-a permutation matches each element :math:`l` in :math:`1, ..., N` to an
-element :math:`\sigma(l)` in :math:`1, ..., N` without repetitions. The
-energies :math:`E^\sigma` correspond to the linking of ring polymers of
-different particles according to the permutations:
-
-.. math::
-
-   E^\sigma = \frac{mP}{2\beta^2 \hbar^2} \sum_{\ell=1}^N \sum_{j=1}^P \left(\mathbf{q}_\ell^j - \mathbf{q}_\ell^{j+1}\right)^2,
-
-where :math:`P` is the number of beads and :math:`\mathbf{q}_\ell^{P+1}=\mathbf{q}_{\sigma(\ell)}^1.`
-
-Hirshberg et. al. showed that the ring polymer potential
-:math:`-\frac{1}{\beta}\textrm{ln}\left[ \frac{1}{N!} \sum_\sigma e ^ {
--\beta E^\sigma } \right]`, which scales exponentially with :math:`N`,
-can be replaced by a potential :math:`V^{[1,N]}` defined through a
-recurrence relation :ref:`(Hirshberg1) <Hirshberg>`:
-
-.. math::
-
-   e ^ { -\beta  V^{[1,N]} } = \frac{1}{N} \sum_{k=1}^N e ^ { -\beta \left(  V^{[1,N-k]} + E^{[N-K+1,N]} \right)}.
-
-Here, :math:`E^{[N-K+1,N]}` is the spring energy of the ring polymer
-obtained by connecting the beads of particles :math:`N - k + 1, N - k +
-2, ..., N` in a cycle.  This potential does not include all :math:`N!`
-permutations, but samples the same bosonic partition function. The
-implemented algorithm in LAMMPS for calculating the potential is the one
-developed by Feldman and Hirshberg, which scales like :math:`N^2+PN`
-:ref:`(Feldman) <Feldman>`.  The forces are calculated as weighted
-averages over the representative permutations, through an algorithm that
-scales the same as the one for the potential calculation, :math:`N^2+PN`
-:ref:`(Feldman) <Feldman>`.  The minimum-image convention is employed on
-the springs to account for periodic boundary conditions; an elaborate
-discussion of the validity of the approximation is available in
-:ref:`(Higer) <HigerFeldman>`.
-
-Restart, fix_modify, output, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-The use of :doc:`binary restart files <restart>` and :doc:`fix_modify
-<fix_modify>` is the same as in :doc:`fix pimd <fix_pimd>`.
-
-Fix *pimd/nvt/bosonic* computes a global 4-vector, which can be accessed by
-various :doc:`output commands <Howto_output>`.  The quantities in
-the global vector are:
-
-   #. the total spring energy of the quasi-beads,
-   #. the current temperature of the classical system of ring polymers,
-   #. the current value of the scalar virial estimator for the kinetic
-      energy of the quantum system :ref:`(Herman) <HermanBB>` (see the justification in the supporting information of :ref:`(Hirshberg2) <HirshbergInvernizzi>`),
-   #. the current value of the scalar primitive estimator for the kinetic
-      energy of the quantum system :ref:`(Hirshberg1) <Hirshberg>`.
-
-The vector values calculated by fix *pimd/nvt/bosonic* are "extensive", except
-for the temperature, which is "intensive".
-
-Fix *pimd/langevin/bosonic* computes a global 6-vector, which can be accessed
-by various :doc:`output commands <Howto_output>`. The quantities in the
-global vector are:
-
-   #. kinetic energy of the beads,
-   #. spring elastic energy of the beads,
-   #. potential energy of the bead,
-   #. total energy of all beads (conserved if *ensemble* is *nve*) if *esynch* is *yes*
-   #. primitive kinetic energy estimator :ref:`(Hirshberg1) <Hirshberg>`
-   #. virial energy estimator :ref:`(Herman) <HermanBB>` (see the justification in the supporting information of :ref:`(Hirshberg2) <HirshbergInvernizzi>`).
-
-The first three are different for different log files, and the others
-are the same for different log files, except for the primitive kinetic
-energy estimator when setting *esynch* to *no*. Then, the primitive
-kinetic energy estimator is obtained by summing over all log files.
-Also note that when *esynch* is set to *no*, the fourth output gives the
-total energy of all beads excluding the spring elastic energy; the total
-classical energy can then be obtained by adding the sum of second output
-over all log files.  All vector values calculated by fix
-*pimd/langevin/bosonic* are "extensive".
-
-For both *pimd/nvt/bosonic* and *pimd/langevin/bosonic*, the contribution of the
-exterior spring to the primitive estimator is printed to the first log
-file.  The contribution of the :math:`P-1` interior springs is printed
-to the other :math:`P-1` log files.  The contribution of the constant
-:math:`\frac{PdN}{2 \beta}` (with :math:`d` being the dimensionality) is
-equally divided over log files.
-
-Restrictions
-""""""""""""
-
-These fixes are part of the REPLICA package.  They are only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package
-<Build_package>` page for more info.
-
-The restrictions of :doc:`fix pimd <fix_pimd>` apply.
-
-Related commands
-""""""""""""""""
-
-:doc:`pimd/nvt <fix_pimd>`, :doc:`pimd/langevin <fix_pimd>`
-
-Default
-"""""""
-
-The keyword defaults for fix *pimd/nvt/bosonic* are method = pimd, fmass = 1.0,
-sp = 1.0, temp = 300.0, and nhc = 2.
-
-The keyword defaults for fix *pimd/langevin/bosonic* are integrator = obabo,
-method = pimd, ensemble = nvt, fmass = 1.0, temp = 298.15, thermostat =
-PILE_L, tau = 1.0, fixcom = yes, esynch = yes, and lj = 1 for all its
-arguments.
-
-----------
-
-.. _book-Tuckerman:
-
-**(Tuckerman)** M. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation (Oxford University Press, 2010)
-
-.. _Hirshberg:
-
-**(Hirshberg1)** B. Hirshberg, V. Rizzi, and M. Parrinello, "Path integral molecular dynamics for bosons," Proc. Natl. Acad. Sci. U. S. A. 116, 21445 (2019)
-
-.. _HirshbergInvernizzi:
-
-**(Hirshberg2)** B. Hirshberg, M. Invernizzi, and M. Parrinello, "Path integral molecular dynamics for fermions: Alleviating the sign problem with the Bogoliubov inequality," J Chem Phys, 152, 171102 (2020)
-
-.. _Feldman:
-
-**(Feldman)** Y. M. Y. Feldman and B. Hirshberg, "Quadratic scaling bosonic path integral molecular dynamics," J. Chem. Phys. 159, 154107 (2023)
-
-.. _HigerFeldman:
-
-**(Higer)** J. Higer, Y. M. Y. Feldman, and B. Hirshberg, "Periodic Boundary Conditions for Bosonic Path Integral Molecular Dynamics," arXiv:2501.17618 (2025)
-
-.. _HermanBB:
-
-**(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).

doc/src/fix_reaxff_species.rst

@@ -207,6 +207,9 @@ 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>`.
 
+This fix supports dynamic groups only if the *Nrepeat* setting is 1,
+i.e. there is no averaging.
+
 ----------
 
 .. include:: accel_styles.rst

doc/src/fix_wall_piston.rst

@@ -33,7 +33,7 @@ Syntax
          *box* = the wall position is defined in simulation box units
 
 ..
-    FIXME: There are several "undocumented" key words for this fix: *rough*,
+    FIXME: There are several "undocumented" keywords for this fix: *rough*,
     *rampNL1*, *rampNL2*, *rampNL3*, *rampNL4*, and *rampNL5*.
 
 Examples

doc/src/min_modify.rst

@@ -98,14 +98,14 @@ all atoms
 
 .. math::
 
-   || \vec{F} ||_{max} = {\rm max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
+   || \vec{F} ||_{max} = \mathrm{max}\left(||\vec{F}_1||, \cdots, ||\vec{F}_N||\right)
 
 The *inf* norm takes the maximum component across the forces of
 all atoms in the system:
 
 .. math::
 
-   || \vec{F} ||_{inf} = {\rm max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
+   || \vec{F} ||_{inf} = \mathrm{max}\left(|F_1^1|, |F_1^2|, |F_1^3| \cdots, |F_N^1|, |F_N^2|, |F_N^3|\right)
 
 For the min styles *spin*, *spin/cg* and *spin/lbfgs*, the force
 norm is replaced by the spin-torque norm.

doc/src/min_spin.rst

@@ -50,9 +50,9 @@ system:
 
 .. math::
 
-   {\Delta t}_{\rm max} = \frac{2\pi}{\kappa \left|\vec{\omega}_{\rm max} \right|}
+   {\Delta t}_\mathrm{max} = \frac{2\pi}{\kappa \left|\vec{\omega}_\mathrm{max} \right|}
 
-with :math:`\left|\vec{\omega}_{\rm max}\right|` the norm of the largest precession
+with :math:`\left|\vec{\omega}_\mathrm{max}\right|` the norm of the largest precession
 frequency in the system (across all processes, and across all replicas if a
 spin/neb calculation is performed).
 

doc/src/minimize.rst

@@ -108,12 +108,12 @@ potential energy of the system as a function of the N atom
 coordinates:
 
 .. math::
- E(r_1,r_2, \ldots ,r_N)  = & \sum_{i,j} E_{\it pair}(r_i,r_j) +
+ E(r_1,r_2, \ldots ,r_N)  = & \sum_{i,j} E_{pair}(r_i,r_j) +
-                              \sum_{ij} E_{\it bond}(r_i,r_j) +
+                              \sum_{ij} E_{bond}(r_i,r_j) +
-                              \sum_{ijk} E_{\it angle}(r_i,r_j,r_k) + \\
+                              \sum_{ijk} E_{angle}(r_i,r_j,r_k) + \\
-                            & \sum_{ijkl} E_{\it dihedral}(r_i,r_j,r_k,r_l) +
+                            & \sum_{ijkl} E_{dihedral}(r_i,r_j,r_k,r_l) +
-                              \sum_{ijkl} E_{\it improper}(r_i,r_j,r_k,r_l) +
+                              \sum_{ijkl} E_{improper}(r_i,r_j,r_k,r_l) +
-                              \sum_i E_{\it fix}(r_i)
+                              \sum_i E_{fix}(r_i)
 
 where the first term is the sum of all non-bonded :doc:`pairwise
 interactions <pair_style>` including :doc:`long-range Coulombic

doc/src/neb_spin.rst

@@ -148,7 +148,7 @@ spin i, :math:`\omega_i^{\nu}` is a rotation angle defined as:
 
 .. math::
 
-   \omega_i^{\nu} = (\nu - 1) \Delta \omega_i {\rm ~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
+   \omega_i^{\nu} = (\nu - 1) \Delta \omega_i \mathrm{~~and~~} \Delta \omega_i = \frac{\omega_i}{Q-1}
 
 with :math:`\nu` the image number, Q the total number of images, and
 :math:`\omega_i` the total rotation between the initial and final spins.

doc/src/pair_aip_water_2dm.rst

@@ -53,14 +53,14 @@ materials as described in :ref:`(Feng1) <Feng1>` and :ref:`(Feng2) <Feng2>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_coul.rst

@@ -241,9 +241,9 @@ summation method, described in :ref:`Wolf <Wolf1>`, given by:
 .. math::
 
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and *erf()* and *erfc()*
 are error-function and complementary error-function terms.  This

doc/src/pair_coul_shield.rst

@@ -40,8 +40,8 @@ the pair style :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
 .. math::
 
    E      = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij} = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
+   V_{ij} = & \mathrm{Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\
-   {\rm Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij}) = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                           70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                           84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                           35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_dpd_ext.rst

@@ -62,8 +62,8 @@ a sum of 3 terms
 
    \mathbf{f}  = & f^C + f^D + f^R \qquad \qquad r < r_c \\
    f^C      = & A_{ij} w(r) \hat{\mathbf{r}}_{ij} \\
-   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \mathbf{v}_{ij} \\
+   f^D      = & - \gamma_{\parallel} w_{\parallel}^2(r) (\hat{\mathbf{r}}_{ij} \cdot \mathbf{v}_{ij}) \hat{\mathbf{r}}_{ij}  - \gamma_{\perp} w_{\perp}^2 (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \mathbf{v}_{ij} \\
-   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^{\rm T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
+   f^R      = & \sigma_{\parallel} w_{\parallel}(r) \frac{\alpha}{\sqrt{\Delta t}} \hat{\mathbf{r}}_{ij}  + \sigma_{\perp} w_{\perp} (r) ( \mathbf{I} - \hat{\mathbf{r}}_{ij} \hat{\mathbf{r}}_{ij}^\mathrm{T} ) \frac{\mathbf{\xi}_{ij}}{\sqrt{\Delta t}}\\
    w(r)     = & 1 - r/r_c \\
 
 where :math:`\mathbf{f}^C` is a conservative force, :math:`\mathbf{f}^D`

doc/src/pair_hbond_dreiding.rst

@@ -68,21 +68,21 @@ force field, given by:
 
 .. math::
 
-   E  = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_{\rm in} \\
+   E  = & \left[LJ(r) | Morse(r) \right] \qquad \qquad \qquad r < r_\mathrm{in} \\
-      = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_{\rm in} < r < r_{\rm out} \\
+      = & S(r) * \left[LJ(r) | Morse(r) \right] \qquad \qquad r_\mathrm{in} < r < r_\mathrm{out} \\
-      = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_{\rm out} \\
+      = & 0 \qquad \qquad \qquad \qquad \qquad \qquad \qquad r > r_\mathrm{out} \\
    LJ(r)  = & AR^{-12}-BR^{-10}cos^n\theta=
          \epsilon\left\lbrace 5\left[ \frac{\sigma}{r}\right]^{12}-
          6\left[ \frac{\sigma}{r}\right]^{10}  \right\rbrace cos^n\theta\\
    Morse(r)  = & D_0\left\lbrace \chi^2 - 2\chi\right\rbrace cos^n\theta=
          D_{0}\left\lbrace e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)}
          \right\rbrace cos^n\theta \\
-   S(r)  = & \frac{ \left[r_{\rm out}^2 - r^2\right]^2
+   S(r)  = & \frac{ \left[r_\mathrm{out}^2 - r^2\right]^2
-   \left[r_{\rm out}^2 + 2r^2 - 3{r_{\rm in}^2}\right]}
+   \left[r_\mathrm{out}^2 + 2r^2 - 3{r_\mathrm{in}^2}\right]}
-   { \left[r_{\rm out}^2 - {r_{\rm in}}^2\right]^3 }
+   { \left[r_\mathrm{out}^2 - {r_\mathrm{in}}^2\right]^3 }
 
-where :math:`r_{\rm in}` is the inner spline distance cutoff,
+where :math:`r_\mathrm{in}` is the inner spline distance cutoff,
-:math:`r_{\rm out}` is the outer distance cutoff, :math:`\theta_c` is
+:math:`r_\mathrm{out}` is the outer distance cutoff, :math:`\theta_c` is
 the angle cutoff, and :math:`n` is the power of the cosine of the angle
 :math:`\theta`.
 
@@ -189,8 +189,8 @@ follows:
 * :math:`\epsilon` (energy units)
 * :math:`\sigma` (distance units)
 * *n* = exponent in formula above
-* distance cutoff :math:`r_{\rm in}` (distance units)
+* distance cutoff :math:`r_\mathrm{in}` (distance units)
-* distance cutoff :math:`r_{\rm out}` (distance units)
+* distance cutoff :math:`r_\mathrm{out}` (distance units)
 * angle cutoff (degrees)
 
 For the *hbond/dreiding/morse* style the list of coefficients is as
@@ -202,7 +202,7 @@ follows:
 * :math:`\alpha` (1/distance units)
 * :math:`r_0` (distance units)
 * *n* = exponent in formula above
-* distance cutoff :math:`r_{\rm in}` (distance units)
+* distance cutoff :math:`r_\mathrm{in}` (distance units)
 * distance cutoff :math:`r_{out}` (distance units)
 * angle cutoff (degrees)
 

doc/src/pair_ilp_graphene_hbn.rst

@@ -44,14 +44,14 @@ in :ref:`(Kolmogorov) <Kolmogorov2>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1

doc/src/pair_ilp_tmd.rst

@@ -41,14 +41,14 @@ as described in :ref:`(Ouyang7) <Ouyang7>` and :ref:`(Jiang) <Jiang>`.
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
@@ -67,7 +67,7 @@ calculating the normals.
    normal vectors used for graphene and h-BN is no longer valid for TMDs.
    In :ref:`(Ouyang7) <Ouyang7>`, a new definition is proposed, where for
    each atom `i`, its six nearest neighboring atoms belonging to the same
-   sub-layer are chosen to define the normal vector `{\bf n}_i`.
+   sub-layer are chosen to define the normal vector `\mathbf{n}_i`.
 
 The parameter file (e.g. TMD.ILP), is intended for use with *metal*
 :doc:`units <units>`, with energies in meV. Two additional parameters,

doc/src/pair_kolmogorov_crespi_full.rst

@@ -37,8 +37,8 @@ No simplification is made,
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
    V_{ij}  = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) \right ] - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \\
-  \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\
+  \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot \mathbf{n}_{i})^2 \\
-  \rho_{ji}^2 = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\
+  \rho_{ji}^2 = & r_{ij}^2 - (\mathbf{r}_{ij}\cdot  \mathbf{n}_{j})^2 \\
   f(\rho) & =  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { (\rho/\delta) }^{2n}
 
 It is important to have a sufficiently large cutoff to ensure smooth

doc/src/pair_lj_cut_coul.rst

@@ -194,9 +194,9 @@ summation method, described in :ref:`Wolf <Wolf3>`, given by:
 .. math::
 
    E_i = \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erfc}(\alpha r_{ij})}{r_{ij}} +
+   \frac{q_i q_j \mathrm{erfc}(\alpha r_{ij})}{r_{ij}} +
    \frac{1}{2} \sum_{j \neq i}
-   \frac{q_i q_j {\rm erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
+   \frac{q_i q_j \mathrm{erf}(\alpha r_{ij})}{r_{ij}} \qquad r < r_c
 
 where :math:`\alpha` is the damping parameter, and erfc() is the
 complementary error-function terms.  This potential is essentially a

doc/src/pair_mesodpd.rst

@@ -200,7 +200,7 @@ force :math:`F_{ij}^C` are expressed as
   \mathbf{F}_{ij}^{D} & = -\gamma {\omega_{D}}(r_{ij})(\mathbf{e}_{ij} \cdot \mathbf{v}_{ij})\mathbf{e}_{ij}  \\
   \mathbf{F}_{ij}^{R} & = \sigma {\omega_{R}}(r_{ij}){\xi_{ij}}\Delta t^{-1/2} \mathbf{e}_{ij} \\
   \omega_{C}(r) & = 1 - r/r_c \\
-  \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^{\rm power_f} \\
+  \omega_{D}(r) & = \omega^2_{R}(r) = (1-r/r_c)^\mathrm{power_f} \\
   \sigma^2 = 2\gamma k_B T
 
 The concentration flux between two tDPD particles includes the Fickian
@@ -211,7 +211,7 @@ by
 
    Q_{ij}^D & = -\kappa_{ij} w_{DC}(r_{ij}) \left( C_i - C_j \right) \\
    Q_{ij}^R & = \epsilon_{ij}\left( C_i + C_j \right) w_{RC}(r_{ij}) \xi_{ij} \\
-   w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^{\rm power_{cc}} \\
+   w_{DC}(r_{ij}) & =w^2_{RC}(r_{ij}) = (1 - r/r_{cc})^\mathrm{power_{cc}} \\
    \epsilon_{ij}^2 & = m_s^2\kappa_{ij}\rho
 
 where the parameters kappa and epsilon determine the strength of the

doc/src/pair_mgpt.rst

@@ -33,7 +33,7 @@ elemental bulk material in the form
 
 .. math::
 
-   E_{\rm tot}({\bf R}_1 \ldots {\bf R}_N) = NE_{\rm vol}(\Omega )
+   E_\mathrm{tot}(\mathbf{R}_1 \ldots \mathbf{R}_N) = NE_\mathrm{vol}(\Omega )
    + \frac{1}{2} \sum _{i,j} \mbox{}^\prime \ v_2(ij;\Omega )
    + \frac{1}{6} \sum _{i,j,k} \mbox{}^\prime \ v_3(ijk;\Omega )
    + \frac{1}{24} \sum _{i,j,k,l} \mbox{}^\prime \ v_4(ijkl;\Omega )

doc/src/pair_saip_metal.rst

@@ -41,14 +41,14 @@ potential (ILP) potential for hetero-junctions formed with hexagonal
 .. math::
 
    E  = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\
-   V_{ij}  = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
+   V_{ij}  = & \mathrm{Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)}
                 \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] -
                  \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
                  \cdot \frac{C_6}{r^6_{ij}} \right \}\\
-   \rho_{ij}^2 = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\
+   \rho_{ij}^2 = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_i)^2 \\
-   \rho_{ji}^2  = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\
+   \rho_{ji}^2  = & r_{ij}^2 - (\mathbf{r}_{ij} \cdot \mathbf{n}_j)^2 \\
    f(\rho)  = &  C e^{ -( \rho / \delta )^2 } \\
-   {\rm Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+   \mathrm{Tap}(r_{ij})  = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
                            70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
                            84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
                            35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
@@ -63,8 +63,8 @@ calculating the normals.
 .. note::
 
    To account for the isotropic nature of the isolated gold atom
-   electron cloud, their corresponding normal vectors (`{\bf n}_i`) are
+   electron cloud, their corresponding normal vectors (`\mathbf{n}_i`) are
-   assumed to lie along the interatomic vector `{\bf r}_ij`. Notably, this
+   assumed to lie along the interatomic vector `\mathbf{r}_ij`. Notably, this
    assumption is suitable for many bulk material surfaces, for
    example, for systems possessing s-type valence orbitals or
    metallic surfaces, whose valence electrons are mostly

doc/src/pair_spin_dipole.rst

@@ -43,7 +43,7 @@ vector omega and mechanical force between particles I and J.
 
 .. math::
 
-   \mathcal{H}_{\rm long} & =
+   \mathcal{H}_\mathrm{long} & =
    -\frac{\mu_{0} \left( \mu_B\right)^2}{4\pi}
    \sum_{i,j,i\neq j}^{N}
     \frac{g_i g_j}{r_{ij}^3}

doc/src/pair_spin_dmi.rst

@@ -52,7 +52,7 @@ particle i:
 .. math::
 
     \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right)
-    ~~{\rm and}~~
+    ~~\mathrm{and}~~
     \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right)
 
 More details about the derivation of these torques/forces are reported in

doc/src/pair_spin_exchange.rst

@@ -94,7 +94,7 @@ submitted to a force :math:`\vec{F}_{i}` for spin-lattice calculations (see
 
    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J}
    \left(r_{ij} \right)\,\vec{s}_{j}
-   ~~{\rm and}~~
+   ~~\mathrm{and}~~
    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}
 

doc/src/region2vmd.rst

@@ -35,7 +35,7 @@ Description
 
 .. versionadded:: TBD
 
-Write a `VMD <https:://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
+Write a `VMD <https://ks.uiuc.edu/Research/vmd/>`_ Tcl script file with
 commands that aim to create a visualization of :doc:`regions <region>`.
 There may be multiple region visualizations stored in a single file.
 

doc/src/timer.rst

@@ -87,7 +87,7 @@ negative, if the timeout time is expired and positive if there
 is time remaining and in this case the value of the variable are
 the number of seconds remaining.
 
-When the *timeout* key word is used a second time, the timer is
+When the *timeout* keyword is used a second time, the timer is
 restarted with a new time limit. The timeout *elapse* value can
 be specified as *off* or *unlimited* to impose a no timeout condition
 (which is the default).  The *elapse* setting can be specified as

doc/src/variable.rst

@@ -51,12 +51,12 @@ Syntax
          thermo keywords = vol, ke, press, etc from :doc:`thermo_style <thermo_style>`
          math operators = (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y,
                           x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x
-         math functions = sqrt(x), exp(x), ln(x), log(x), abs(x),
+         math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x),
                           sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x),
                           random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z),
                           ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z),
                           logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c),
-                          vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x)
+                          vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)
          group functions = count(group), mass(group), charge(group),
                            xcm(group,dim), vcm(group,dim), fcm(group,dim),
                            bound(group,dir), gyration(group), ke(group),
@@ -541,7 +541,7 @@ variables.
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Math operators         | (), -x, x+y, x-y, x\*y, x/y, x\^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x \|\| y, x \|\^ y, !x                                                                                                                                                                                                                                       |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
-| Math functions         | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z), sign(x)  |
+| Math functions         | sqrt(x), exp(x), ln(x), log(x), abs(x), sign(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ternary(x,y,z), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), logfreq3(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z)  |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
 | Group functions        | count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim)                                                                                                                                                                             |
 +------------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@@ -692,6 +692,11 @@ sqrt() of the product of one atom's y and z coordinates.
 Most of the math functions perform obvious operations.  The ln() is
 the natural log; log() is the base 10 log.
 
+.. versionadded:: 4Feb2025
+
+The sign(x) function returns 1.0 if the value is greater than or equal
+to 0.0, and -1.0 otherwise.
+
 The random(x,y,z) function takes 3 arguments: x = lo, y = hi, and z =
 seed.  It generates a uniform random number between lo and hi.  The
 normal(x,y,z) function also takes 3 arguments: x = mu, y = sigma, and
@@ -860,9 +865,6 @@ run, according to one of these formulas, where omega = 2 PI / period:
 
 where dt = the timestep size.
 
-The sign(x) function returns 1.0 if the value is greater than or equal
-to 0.0, and -1.0 otherwise.
-
 The run begins on startstep.  Startstep can span multiple runs, using
 the *start* keyword of the :doc:`run <run>` command.  See the :doc:`run
 <run>` command for details of how to do this.  Note that the

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <8.2.0
+Sphinx >= 5.3.0, <8.3.0
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 sphinx-design

doc/utils/sphinx-config/conf.py.in

@@ -208,13 +208,11 @@ html_favicon = '_static/lammps.ico'
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ['_static',]
 
 # These paths are either relative to html_static_path
 # or fully qualified paths (eg. https://...)
-html_css_files = [
+html_css_files = ['css/lammps.css',]
-    'css/lammps.css',
-]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -290,7 +288,7 @@ rst_prolog = r"""
 
 .. only:: html
 
-   :math:`\renewcommand{\AA}{\text{Å}}`
+   :math:`\renewcommand{\AA}{\textup{\r{A}}`
 
 .. role:: lammps(code)
     :language: LAMMPS

doc/utils/sphinx-config/false_positives.txt

@@ -1331,6 +1331,7 @@ geturl
 gewald
 Gezelter
 gfile
+gflag
 Gflop
 gfortran
 ghostneigh
@@ -2964,6 +2965,7 @@ pKa
 pKb
 pKs
 planeforce
+plastically
 Plathe
 Plimpton
 plog
@@ -3266,6 +3268,7 @@ rewrap
 rezwanur
 rfac
 rfile
+rflag
 rg
 Rg
 Rhaphson

examples/COUPLE/multiple/in.chain

@@ -1,5 +1,5 @@
 # FENE beadspring benchmark
-
+variable        t index 1.0
 units		lj
 atom_style	bond
 special_bonds   fene

examples/PACKAGES/atc/elastic/Au_u3.eam

@@ -0,0 +1 @@
+../../../../potentials/Au_u3.eam

examples/PACKAGES/pafi/in.pafi

@@ -9,7 +9,7 @@ read_data pafipath.4.data fix pa NULL PafiPath
 
 ## EAM potential
 pair_style    eam/fs
-pair_coeff * * ../../../../potentials/Fe_mm.eam.fs Fe
+pair_coeff * * Fe_mm.eam.fs Fe
 
 mass * 55.85
 thermo 100

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++

@@ -0,0 +1,2 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
+Running on 4 partitions of processors

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.0

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -103,8 +104,8 @@ Initializing PI Langevin equation thermostat...
       3     9.11206647e-03 5.00000000e+01 9.95012479e-01 9.97505201e-02
   PILE_L thermostat successfully initialized!
 
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -208,20 +209,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   9.2042324e-06  1.780703e-05   0.00083221292
         99   9.5058078e-06  1.8141862e-05  0.00082913227
        100   9.8087647e-06  1.8457846e-05  0.00082619877
-Loop time of 0.122922 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00116399 on 1 procs for 100 steps with 3 atoms
 
-Performance: 35144210.362 fs/day, 0.000 hours/fs, 813.523 timesteps/s, 2.441 katom-step/s
+Performance: 3711359336.904 fs/day, 0.000 hours/fs, 85911.096 timesteps/s, 257.733 katom-step/s
-70.1% CPU use with 1 MPI tasks x no OpenMP threads
+89.8% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.1593e-05 | 1.1593e-05 | 1.1593e-05 |   0.0 |  0.01
+Neigh   | 1.292e-06  | 1.292e-06  | 1.292e-06  |   0.0 |  0.11
-Comm    | 9.2183e-05 | 9.2183e-05 | 9.2183e-05 |   0.0 |  0.07
+Comm    | 1.2305e-05 | 1.2305e-05 | 1.2305e-05 |   0.0 |  1.06
-Output  | 0.023243   | 0.023243   | 0.023243   |   0.0 | 18.91
+Output  | 0.00018105 | 0.00018105 | 0.00018105 |   0.0 | 15.55
-Modify  | 0.099386   | 0.099386   | 0.099386   |   0.0 | 80.85
+Modify  | 0.00090255 | 0.00090255 | 0.00090255 |   0.0 | 77.54
-Other   |            | 0.0001896  |            |       |  0.15
+Other   |            | 6.68e-05   |            |       |  5.74
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -234,3 +235,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 33
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.1

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   2.5769956e-05  1.780703e-05   0.00083221292
         99   2.624134e-05   1.8141862e-05  0.00082913227
        100   2.6731735e-05  1.8457846e-05  0.00082619877
-Loop time of 0.122878 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.0011782 on 1 procs for 100 steps with 3 atoms
 
-Performance: 35156789.883 fs/day, 0.000 hours/fs, 813.815 timesteps/s, 2.441 katom-step/s
+Performance: 3666606971.137 fs/day, 0.000 hours/fs, 84875.161 timesteps/s, 254.625 katom-step/s
-46.7% CPU use with 1 MPI tasks x no OpenMP threads
+88.4% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.9787e-05 | 1.9787e-05 | 1.9787e-05 |   0.0 |  0.02
+Neigh   | 1.773e-06  | 1.773e-06  | 1.773e-06  |   0.0 |  0.15
-Comm    | 9.2033e-05 | 9.2033e-05 | 9.2033e-05 |   0.0 |  0.07
+Comm    | 1.4979e-05 | 1.4979e-05 | 1.4979e-05 |   0.0 |  1.27
-Output  | 0.0022584  | 0.0022584  | 0.0022584  |   0.0 |  1.84
+Output  | 0.00021888 | 0.00021888 | 0.00021888 |   0.0 | 18.58
-Modify  | 0.12033    | 0.12033    | 0.12033    |   0.0 | 97.93
+Modify  | 0.00086503 | 0.00086503 | 0.00086503 |   0.0 | 73.42
-Other   |            | 0.0001755  |            |       |  0.14
+Other   |            | 7.754e-05  |            |       |  6.58
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -226,3 +227,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 44
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.2

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 2
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   1.8568337e-05  1.780703e-05   0.00083221292
         99   1.9188379e-05  1.8141862e-05  0.00082913227
        100   1.9789011e-05  1.8457846e-05  0.00082619877
-Loop time of 0.112003 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00116163 on 1 procs for 100 steps with 3 atoms
 
-Performance: 38570373.396 fs/day, 0.000 hours/fs, 892.833 timesteps/s, 2.678 katom-step/s
+Performance: 3718915419.639 fs/day, 0.000 hours/fs, 86086.005 timesteps/s, 258.258 katom-step/s
-52.7% CPU use with 1 MPI tasks x no OpenMP threads
+89.6% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.4356e-05 | 1.4356e-05 | 1.4356e-05 |   0.0 |  0.01
+Neigh   | 1.582e-06  | 1.582e-06  | 1.582e-06  |   0.0 |  0.14
-Comm    | 9.7936e-05 | 9.7936e-05 | 9.7936e-05 |   0.0 |  0.09
+Comm    | 1.3306e-05 | 1.3306e-05 | 1.3306e-05 |   0.0 |  1.15
-Output  | 0.0017373  | 0.0017373  | 0.0017373  |   0.0 |  1.55
+Output  | 0.00017996 | 0.00017996 | 0.00017996 |   0.0 | 15.49
-Modify  | 0.10997    | 0.10997    | 0.10997    |   0.0 | 98.19
+Modify  | 0.00090771 | 0.00090771 | 0.00090771 |   0.0 | 78.14
-Other   |            | 0.0001804  |            |       |  0.16
+Other   |            | 5.907e-05  |            |       |  5.09
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -226,3 +227,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 41
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_langevin/log.13Mar2025.g++.3

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 3
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -95,8 +96,8 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              1.3661449e-08  0.0009918329 
@@ -200,20 +201,20 @@ Per MPI rank memory allocation (min/avg/max) = 2.801 | 2.801 | 2.801 Mbytes
         98   2.5288512e-05  1.780703e-05   0.00083221292
         99   2.5384836e-05  1.8141862e-05  0.00082913227
        100   2.5401412e-05  1.8457846e-05  0.00082619877
-Loop time of 0.122921 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00116067 on 1 procs for 100 steps with 3 atoms
 
-Performance: 35144393.915 fs/day, 0.000 hours/fs, 813.528 timesteps/s, 2.441 katom-step/s
+Performance: 3721997782.310 fs/day, 0.000 hours/fs, 86157.356 timesteps/s, 258.472 katom-step/s
-88.8% CPU use with 1 MPI tasks x no OpenMP threads
+88.3% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 1.5885e-05 | 1.5885e-05 | 1.5885e-05 |   0.0 |  0.01
+Neigh   | 1.441e-06  | 1.441e-06  | 1.441e-06  |   0.0 |  0.12
-Comm    | 9.4707e-05 | 9.4707e-05 | 9.4707e-05 |   0.0 |  0.08
+Comm    | 1.2111e-05 | 1.2111e-05 | 1.2111e-05 |   0.0 |  1.04
-Output  | 0.0027076  | 0.0027076  | 0.0027076  |   0.0 |  2.20
+Output  | 0.00018148 | 0.00018148 | 0.00018148 |   0.0 | 15.64
-Modify  | 0.11993    | 0.11993    | 0.11993    |   0.0 | 97.57
+Modify  | 0.0009054  | 0.0009054  | 0.0009054  |   0.0 | 78.01
-Other   |            | 0.0001738  |            |       |  0.14
+Other   |            | 6.023e-05  |            |       |  5.19
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -226,3 +227,4 @@ Total # of neighbors = 0
 Ave neighs/atom = 0
 Neighbor list builds = 42
 Dangerous builds = 0
+Total wall time: 0:00:00

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++

@@ -0,0 +1,2 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
+Running on 4 partitions of processors

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.0

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 0
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,11 +100,11 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
 Fix pimd/nvt -P/(beta^2 * hbar^2) =       -2.2139311e-05 (kcal/mol/A^2)
 
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024794798
@@ -207,20 +208,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.4842314e-06  1.8940408e-06  0.0002348915 
         99   7.622805e-06   1.9289045e-06  0.00023466684
        100   7.76221e-06    1.9639756e-06  0.00023444136
-Loop time of 0.00940749 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00193128 on 1 procs for 100 steps with 3 atoms
 
-Performance: 459208566.791 fs/day, 0.000 hours/fs, 10629.828 timesteps/s, 31.889 katom-step/s
+Performance: 2236858456.568 fs/day, 0.000 hours/fs, 51779.131 timesteps/s, 155.337 katom-step/s
-90.3% CPU use with 1 MPI tasks x no OpenMP threads
+36.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.466e-06  | 8.466e-06  | 8.466e-06  |   0.0 |  0.09
+Neigh   | 1.454e-06  | 1.454e-06  | 1.454e-06  |   0.0 |  0.08
-Comm    | 7.8365e-05 | 7.8365e-05 | 7.8365e-05 |   0.0 |  0.83
+Comm    | 2.3033e-05 | 2.3033e-05 | 2.3033e-05 |   0.0 |  1.19
-Output  | 0.0012482  | 0.0012482  | 0.0012482  |   0.0 | 13.27
+Output  | 0.00030824 | 0.00030824 | 0.00030824 |   0.0 | 15.96
-Modify  | 0.0079193  | 0.0079193  | 0.0079193  |   0.0 | 84.18
+Modify  | 0.001541   | 0.001541   | 0.001541   |   0.0 | 79.79
-Other   |            | 0.0001532  |            |       |  1.63
+Other   |            | 5.754e-05  |            |       |  2.98
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.1

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 1
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024796164
@@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.3002707e-06  1.8531354e-06  0.00024148118
         99   7.4315008e-06  1.88617e-06    0.00024137268
        100   7.563358e-06   1.9193596e-06  0.00024126398
-Loop time of 0.00941353 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00190888 on 1 procs for 100 steps with 3 atoms
 
-Performance: 458913876.206 fs/day, 0.000 hours/fs, 10623.006 timesteps/s, 31.869 katom-step/s
+Performance: 2263110719.025 fs/day, 0.000 hours/fs, 52386.822 timesteps/s, 157.160 katom-step/s
-50.9% CPU use with 1 MPI tasks x no OpenMP threads
+0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.215e-06  | 8.215e-06  | 8.215e-06  |   0.0 |  0.09
+Neigh   | 2.774e-06  | 2.774e-06  | 2.774e-06  |   0.0 |  0.15
-Comm    | 7.7692e-05 | 7.7692e-05 | 7.7692e-05 |   0.0 |  0.83
+Comm    | 2.3215e-05 | 2.3215e-05 | 2.3215e-05 |   0.0 |  1.22
-Output  | 0.0047662  | 0.0047662  | 0.0047662  |   0.0 | 50.63
+Output  | 0.00042246 | 0.00042246 | 0.00042246 |   0.0 | 22.13
-Modify  | 0.004407   | 0.004407   | 0.004407   |   0.0 | 46.82
+Modify  | 0.0013744  | 0.0013744  | 0.0013744  |   0.0 | 72.00
-Other   |            | 0.0001545  |            |       |  1.64
+Other   |            | 8.601e-05  |            |       |  4.51
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.2

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 2
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024796164
@@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.1356907e-06  1.7335027e-06  0.0002297417 
         99   7.2605738e-06  1.7643404e-06  0.00022943234
        100   7.3859169e-06  1.7952968e-06  0.00022912226
-Loop time of 0.00941372 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00195857 on 1 procs for 100 steps with 3 atoms
 
-Performance: 458904516.311 fs/day, 0.000 hours/fs, 10622.790 timesteps/s, 31.868 katom-step/s
+Performance: 2205688634.372 fs/day, 0.000 hours/fs, 51057.607 timesteps/s, 153.173 katom-step/s
-24.7% CPU use with 1 MPI tasks x no OpenMP threads
+39.2% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.785e-06  | 8.785e-06  | 8.785e-06  |   0.0 |  0.09
+Neigh   | 1.602e-06  | 1.602e-06  | 1.602e-06  |   0.0 |  0.08
-Comm    | 7.9921e-05 | 7.9921e-05 | 7.9921e-05 |   0.0 |  0.85
+Comm    | 1.6951e-05 | 1.6951e-05 | 1.6951e-05 |   0.0 |  0.87
-Output  | 0.0071119  | 0.0071119  | 0.0071119  |   0.0 | 75.55
+Output  | 0.00032627 | 0.00032627 | 0.00032627 |   0.0 | 16.66
-Modify  | 0.0020558  | 0.0020558  | 0.0020558  |   0.0 | 21.84
+Modify  | 0.0015486  | 0.0015486  | 0.0015486  |   0.0 | 79.07
-Other   |            | 0.0001572  |            |       |  1.67
+Other   |            | 6.514e-05  |            |       |  3.33
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/pimd_bosonic/harmonic_trap_nvt/log.13Mar2025.g++.3

@@ -1,5 +1,6 @@
-LAMMPS (4 Feb 2025)
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-344-g0a4a2f6deb-modified)
 Processor partition = 3
+  using 1 OpenMP thread(s) per MPI task
 # Units and dimensions
 units        electron
 dimension    3
@@ -99,9 +100,9 @@ thermo_style custom step pe v_virial v_prim_kinetic
 thermo          1
 
 run             100
-WARNING: No fixes with time integration, atoms won't move (../verlet.cpp:60)
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
-WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (../atom.cpp:2444)
+WARNING: No pairwise cutoff or binsize set. Atom sorting therefore disabled. (src/atom.cpp:2444)
-WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (../comm_brick.cpp:212)
+WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:212)
 Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
    Step         PotEng        v_virial    v_prim_kinetic
          0   0              0              0.00024796164
@@ -205,20 +206,20 @@ Per MPI rank memory allocation (min/avg/max) = 9.176 | 9.176 | 9.176 Mbytes
         98   7.2937187e-06  1.8407787e-06  0.00023702765
         99   7.4250201e-06  1.8736806e-06  0.00023685186
        100   7.5569619e-06  1.9067398e-06  0.00023667607
-Loop time of 0.00939597 on 1 procs for 100 steps with 3 atoms
+Loop time of 0.00197094 on 1 procs for 100 steps with 3 atoms
 
-Performance: 459771778.655 fs/day, 0.000 hours/fs, 10642.865 timesteps/s, 31.929 katom-step/s
+Performance: 2191851993.165 fs/day, 0.000 hours/fs, 50737.315 timesteps/s, 152.212 katom-step/s
-25.2% CPU use with 1 MPI tasks x no OpenMP threads
+37.5% CPU use with 1 MPI tasks x 1 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
 Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 8.404e-06  | 8.404e-06  | 8.404e-06  |   0.0 |  0.09
+Neigh   | 1.652e-06  | 1.652e-06  | 1.652e-06  |   0.0 |  0.08
-Comm    | 8.6872e-05 | 8.6872e-05 | 8.6872e-05 |   0.0 |  0.92
+Comm    | 1.7965e-05 | 1.7965e-05 | 1.7965e-05 |   0.0 |  0.91
-Output  | 0.0071309  | 0.0071309  | 0.0071309  |   0.0 | 75.89
+Output  | 0.00036011 | 0.00036011 | 0.00036011 |   0.0 | 18.27
-Modify  | 0.0020085  | 0.0020085  | 0.0020085  |   0.0 | 21.38
+Modify  | 0.0015231  | 0.0015231  | 0.0015231  |   0.0 | 77.28
-Other   |            | 0.0001612  |            |       |  1.72
+Other   |            | 6.806e-05  |            |       |  3.45
 
 Nlocal:              3 ave           3 max           3 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

examples/PACKAGES/ti/in.ti_spring

@@ -13,7 +13,7 @@
   create_atoms      1 box
 
   pair_style        eam/alloy
-  pair_coeff        * * ../../../../potentials/Cu_mishin1.eam.alloy Cu
+  pair_coeff        * * Cu_mishin1.eam.alloy Cu
 #------------------------------------------------------------------------------#
 
 

examples/SPIN/read_restart/in.spin.read_data

@@ -7,6 +7,7 @@ atom_style 	spin
 # necessary for the serial algorithm (sametag)
 atom_modify     map array
 read_data       Norm_randXY_8x8x32.data
+replicate       1 1 2
 
 mass            1 58.93
 
@@ -40,6 +41,6 @@ thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
 thermo_modify   format float %20.15g
 
 compute         outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump            1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
+#dump_modify     1 sort id
 run             100

examples/SPIN/read_restart/in.spin.write_restart

@@ -18,7 +18,7 @@ create_atoms 	1 box
 
 mass            1 58.93
 
-set 		group all spin/random 31 1.72
+set             group all spin/atom/random 31 1.72
 
 pair_style      spin/exchange 4.0
 pair_coeff      * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
@@ -48,7 +48,7 @@ thermo_style    custom step time v_magnorm pe v_emag temp etotal
 thermo          100
 
 compute         outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
+#dump_modify     100 sort id
 run             1000
 write_restart   restart_hcp_cobalt.equil

examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.1

@@ -0,0 +1,136 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units           metal
+dimension       3
+boundary        p p p
+
+atom_style      spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+read_data       Norm_randXY_8x8x32.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (15 28.32 13.68)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1024 atoms
+  reading velocities ...
+  1024 velocities
+  read_data CPU = 0.004 seconds
+replicate       1 1 2
+Replication is creating a 1x1x2 = 2 times larger system...
+  orthogonal box = (0 0 0) to (15 28.32 27.36)
+  1 by 1 by 1 MPI processor grid
+  2048 atoms
+  replicate CPU = 0.001 seconds
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs and computes
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     1 sort id
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 5 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 9.082 | 9.082 | 9.082 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+         0                     0     0.99566943155533     116726.359107918    -852.392312873949     34.9207785637842                    0     116726.359107918
+        20                 0.002    0.995669416541629     70905.5692189811    -849.222504107045      34.647400481739     172820.122486868     116632.998844426
+        40                 0.004    0.995669401356638     71221.2391274615    -848.368415908416     34.9759984641547     171555.103338675     116613.950357609
+        60                 0.006    0.995669394598344     69647.7523345612    -845.585158124559      36.100016238044     177502.681559427     116614.166097826
+        80                 0.008    0.995669395756676     107415.560454437    -846.200871523815     37.9775024824566     35031.4099604677     116684.714477685
+       100                  0.01    0.995669403283478     63849.6798250643    -836.341677782106      39.680777051272     199492.565587335     116634.518317396
+Loop time of 2.97847 on 1 procs for 100 steps with 2048 atoms
+
+Performance: 0.290 ns/day, 82.735 hours/ns, 33.574 timesteps/s, 68.760 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.0361     | 1.0361     | 1.0361     |   0.0 | 34.79
+Neigh   | 0.78559    | 0.78559    | 0.78559    |   0.0 | 26.38
+Comm    | 0.013262   | 0.013262   | 0.013262   |   0.0 |  0.45
+Output  | 0.00026908 | 0.00026908 | 0.00026908 |   0.0 |  0.01
+Modify  | 1.1415     | 1.1415     | 1.1415     |   0.0 | 38.33
+Other   |            | 0.001761   |            |       |  0.06
+
+Nlocal:           2048 ave        2048 max        2048 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           7952 ave        7952 max        7952 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:         314944 ave      314944 max      314944 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:       629888 ave      629888 max      629888 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 629888
+Ave neighs/atom = 307.5625
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:03

examples/SPIN/read_restart/log.10Mar25.spin.read_data.g++.4

@@ -0,0 +1,136 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units           metal
+dimension       3
+boundary        p p p
+
+atom_style      spin
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+read_data       Norm_randXY_8x8x32.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (15 28.32 13.68)
+  2 by 2 by 1 MPI processor grid
+  reading atoms ...
+  1024 atoms
+  reading velocities ...
+  1024 velocities
+  read_data CPU = 0.004 seconds
+replicate       1 1 2
+Replication is creating a 1x1x2 = 2 times larger system...
+  orthogonal box = (0 0 0) to (15 28.32 27.36)
+  1 by 2 by 2 MPI processor grid
+  2048 atoms
+  replicate CPU = 0.002 seconds
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs and computes
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     1 sort id
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 5 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.812 | 5.812 | 5.812 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+         0                     0    0.995669431555328     116726.359107923     -852.39231287395     34.9207785637843                    0     116726.359107923
+        20                 0.002    0.995669419512638     70905.5692199804    -849.222502855646     34.6474282239503     172820.122483292     116632.998844479
+        40                 0.004    0.995669419108591     71221.2391285209    -848.368412494784       34.97611050919     171555.103335676     116613.950357875
+        60                 0.006     0.99566940895435     69647.7523345112    -845.585157291247     36.1001312564486     177502.681560664     116614.166098104
+        80                 0.008    0.995669417344697     107415.560454912    -846.200874451992     37.9776090859263     35031.4099596403     116684.714477941
+       100                  0.01    0.995669427709463     63849.6798245944    -836.341678212079     39.6809090980074     199492.565591024     116634.518317902
+Loop time of 0.991506 on 4 procs for 100 steps with 2048 atoms
+
+Performance: 0.871 ns/day, 27.542 hours/ns, 100.857 timesteps/s, 206.554 katom-step/s
+99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.31016    | 0.31287    | 0.31496    |   0.3 | 31.56
+Neigh   | 0.21999    | 0.22957    | 0.23793    |   1.7 | 23.15
+Comm    | 0.015231   | 0.025975   | 0.036137   |   6.0 |  2.62
+Output  | 0.00012037 | 0.00014855 | 0.0001849  |   0.0 |  0.01
+Modify  | 0.4213     | 0.42166    | 0.42201    |   0.0 | 42.53
+Other   |            | 0.001272   |            |       |  0.13
+
+Nlocal:            512 ave         521 max         503 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Nghost:           4112 ave        4121 max        4103 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:          78736 ave       80265 max       77207 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+FullNghs:       157472 ave      160276 max      154668 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+
+Total # of neighbors = 629888
+Ave neighs/atom = 307.5625
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:01

examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.1

@@ -0,0 +1,135 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# start a spin-lattice simulation from a data file
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+read_restart    restart_hcp_cobalt.equil
+Reading restart file ...
+  restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025
+  restoring atom style spin from restart
+  orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 1 by 1 MPI processor grid
+  restoring pair style spin/exchange from restart
+  500 atoms
+  read_restart CPU = 0.000 seconds
+
+# setting mass, mag. moments, and interactions
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 4 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 5.255 | 5.255 | 5.255 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+      1000                   0.1   0.0932563992120983    -2200.23506043127    -5.23510819573568      2608.1272233749                    0    -2200.23506043127
+      1020                 0.102   0.0932564226983496    -2200.24431693921    -5.24438874766875     2636.89284253705    0.143502110493468    -2200.23506093651
+      1040                 0.104   0.0932564330551733    -2200.27026761331    -5.27068764778909     2646.09012775508    0.545814389665464    -2200.23506214178
+      1060                 0.106   0.0932564065525508    -2200.30841491752    -5.31025431862422     2627.26990645217     1.13721564075693    -2200.23506358487
+      1080                 0.108   0.0932563850278094    -2200.35339675793    -5.35874497582981     2585.24230543411     1.83458183455181    -2200.23506473927
+      1100                  0.11   0.0932563977118321    -2200.40087596139    -5.41289411193204     2540.00857034711      2.5706738278606    -2200.23506541119
+Loop time of 0.473574 on 1 procs for 100 steps with 500 atoms
+
+Performance: 1.824 ns/day, 13.155 hours/ns, 211.160 timesteps/s, 105.580 katom-step/s
+98.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12025    | 0.12025    | 0.12025    |   0.0 | 25.39
+Neigh   | 0.14912    | 0.14912    | 0.14912    |   0.0 | 31.49
+Comm    | 0.0047587  | 0.0047587  | 0.0047587  |   0.0 |  1.00
+Output  | 0.07234    | 0.07234    | 0.07234    |   0.0 | 15.28
+Modify  | 0.12645    | 0.12645    | 0.12645    |   0.0 | 26.70
+Other   |            | 0.0006494  |            |       |  0.14
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           2534 ave        2534 max        2534 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          36500 ave       36500 max       36500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:        73000 ave       73000 max       73000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 73000
+Ave neighs/atom = 146
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.10Mar25.spin.restart.g++.4

@@ -0,0 +1,136 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# start a spin-lattice simulation from a data file
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+read_restart    restart_hcp_cobalt.equil
+Reading restart file ...
+  restart file = 4 Feb 2025, LAMMPS = 4 Feb 2025
+WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:628)
+  restoring atom style spin from restart
+  orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 2 by 2 MPI processor grid
+  restoring pair style spin/exchange from restart
+  500 atoms
+  read_restart CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions
+
+mass            1 58.93
+
+pair_style      hybrid/overlay eam/alloy spin/exchange 4.0
+pair_coeff      * * eam/alloy Co_PurjaPun_2012.eam.alloy Co
+pair_coeff      * * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        1.0 bin
+neigh_modify    every 1 check no delay 0
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 0.0 0.0 21
+
+fix             3 all nve/spin lattice moving
+timestep        0.0001
+
+# define outputs
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo          20
+thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
+thermo_modify   format float %20.15g
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+
+run             100
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 7.499539
+  ghost atom cutoff = 7.499539
+  binsize = 3.7497695, bins = 4 6 6
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 7.499539
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Dump 100 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 5.188 | 5.188 | 5.188 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag         v_tmag          Temp          TotEng    
+      1000                   0.1   0.0932563992120983    -2200.23506043087    -5.23510819573568      2608.1272233749                    0    -2200.23506043087
+      1020                 0.102   0.0932564663999882    -2200.24431693996    -5.24438874845296     2636.89226887198     0.14350212264756    -2200.23506093648
+      1040                 0.104   0.0932565837400281    -2200.27026761822    -5.27068765273516     2646.08966888271    0.545814465748645    -2200.23506214179
+      1060                 0.106   0.0932567073488227    -2200.30841492456    -5.31025432590717     2627.27001685206     1.13721574991944    -2200.23506358486
+      1080                 0.108   0.0932567401022577    -2200.35339675946    -5.35874497805351     2585.24242001276     1.83458185842719    -2200.23506473925
+      1100                  0.11   0.0932566884738387     -2200.4008759633    -5.41289411525345     2540.00813568378     2.57067385759474    -2200.23506541119
+Loop time of 0.180477 on 4 procs for 100 steps with 500 atoms
+
+Performance: 4.787 ns/day, 5.013 hours/ns, 554.088 timesteps/s, 277.044 katom-step/s
+97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.033968   | 0.034363   | 0.035109   |   0.2 | 19.04
+Neigh   | 0.035043   | 0.03728    | 0.040013   |   0.9 | 20.66
+Comm    | 0.0049574  | 0.0073867  | 0.0089549  |   1.7 |  4.09
+Output  | 0.021087   | 0.023594   | 0.026417   |   1.3 | 13.07
+Modify  | 0.074785   | 0.07749    | 0.079892   |   0.7 | 42.94
+Other   |            | 0.0003627  |            |       |  0.20
+
+Nlocal:            125 ave         136 max         117 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:           1387 ave        1395 max        1376 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs:           9125 ave        9972 max        8559 min
+Histogram: 1 0 1 1 0 0 0 0 0 1
+FullNghs:        18250 ave       19856 max       17082 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+
+Total # of neighbors = 73000
+Ave neighs/atom = 146
+Neighbor list builds = 100
+Dangerous builds not checked
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.1

@@ -0,0 +1,142 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# fcc cobalt in a 3d periodic box
+
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 1 by 1 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  create_atoms CPU = 0.000 seconds
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.93
+
+set             group all spin/atom/random 31 1.72
+Setting atom values ...
+  500 settings made for spin/atom/random
+
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 100.0 0.01 21
+
+fix             3 all nve/spin lattice frozen
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm pe v_emag temp etotal
+thermo          100
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     100 sort id
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.1
+  ghost atom cutoff = 4.1
+  binsize = 2.05, bins = 7 11 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.78 | 4.78 | 4.78 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag          Temp          TotEng    
+         0   0              0.076558814    0.89911794     0.89911794     0              0.89911794   
+       100   0.01           0.077627966    0.36694275     0.36694275     0              0.36694275   
+       200   0.02           0.076678387   -0.20241504    -0.20241504     0             -0.20241504   
+       300   0.03           0.079174207   -0.67593525    -0.67593525     0             -0.67593525   
+       400   0.04           0.085031074   -1.5172826     -1.5172826      0             -1.5172826    
+       500   0.05           0.087026279   -2.042653      -2.042653       0             -2.042653     
+       600   0.06           0.087064628   -2.6297295     -2.6297295      0             -2.6297295    
+       700   0.07           0.089787949   -3.3144767     -3.3144767      0             -3.3144767    
+       800   0.08           0.091698615   -4.028707      -4.028707       0             -4.028707     
+       900   0.09           0.090031988   -4.6007241     -4.6007241      0             -4.6007241    
+      1000   0.1            0.093256399   -5.2351082     -5.2351082      0             -5.2351082    
+Loop time of 0.710555 on 1 procs for 1000 steps with 500 atoms
+
+Performance: 12.160 ns/day, 1.974 hours/ns, 1407.350 timesteps/s, 703.675 katom-step/s
+99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.12852    | 0.12852    | 0.12852    |   0.0 | 18.09
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.012387   | 0.012387   | 0.012387   |   0.0 |  1.74
+Output  | 0.00014522 | 0.00014522 | 0.00014522 |   0.0 |  0.02
+Modify  | 0.56835    | 0.56835    | 0.56835    |   0.0 | 79.99
+Other   |            | 0.001145   |            |       |  0.16
+
+Nlocal:            500 ave         500 max         500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1221 ave        1221 max        1221 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:        10000 ave       10000 max       10000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10000
+Ave neighs/atom = 20
+Neighbor list builds = 0
+Dangerous builds = 0
+write_restart   restart_hcp_cobalt.equil
+System init for write_restart ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.10Mar25.spin.write_restart.g++.4

@@ -0,0 +1,142 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-212-g01698ddc2e-modified)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# fcc cobalt in a 3d periodic box
+
+units           metal
+atom_style      spin
+
+dimension       3
+boundary        p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify     map array
+
+lattice         hcp 2.5071
+Lattice spacing in x,y,z = 2.5071 4.3424246 4.0940772
+region          box block 0.0 5.0 0.0 5.0 0.0 5.0
+create_box      1 box
+Created orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  1 by 2 by 2 MPI processor grid
+create_atoms    1 box
+Created 500 atoms
+  using lattice units in orthogonal box = (0 0 0) to (12.5355 21.712123 20.470386)
+  create_atoms CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions for cobalt
+
+mass            1 58.93
+
+set             group all spin/atom/random 31 1.72
+Setting atom values ...
+  500 settings made for spin/atom/random
+
+pair_style      spin/exchange 4.0
+pair_coeff      * * exchange 4.0 0.3593 1.135028015e-05 1.064568567
+
+neighbor        0.1 bin
+neigh_modify    every 10 check yes delay 20
+
+fix             1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin/spin 100.0 0.01 21
+
+fix             3 all nve/spin lattice frozen
+timestep        0.0001
+
+# compute and output options
+
+compute         out_mag    all spin
+compute         out_pe     all pe
+compute         out_ke     all ke
+compute         out_temp   all temp
+
+variable        magz      equal c_out_mag[3]
+variable        magnorm   equal c_out_mag[4]
+variable        emag      equal c_out_mag[5]
+variable        tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_magnorm pe v_emag temp etotal
+thermo          100
+
+compute         outsp all property/atom spx spy spz sp fmx fmy fmz
+#dump            100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
+#dump_modify     100 sort id
+run             1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.1
+  ghost atom cutoff = 4.1
+  binsize = 2.05, bins = 7 11 10
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.732 | 4.732 | 4.733 Mbytes
+   Step          Time        v_magnorm        PotEng         v_emag          Temp          TotEng    
+         0   0              0.076558814    0.89911794     0.89911794     0              0.89911794   
+       100   0.01           0.078299852    0.44131103     0.44131103     0              0.44131103   
+       200   0.02           0.081260369   -0.2174146     -0.2174146      0             -0.2174146    
+       300   0.03           0.081195064   -0.87039697    -0.87039697     0             -0.87039697   
+       400   0.04           0.087298284   -1.7069593     -1.7069593      0             -1.7069593    
+       500   0.05           0.087663192   -2.1882865     -2.1882865      0             -2.1882865    
+       600   0.06           0.091713114   -2.926766      -2.926766       0             -2.926766     
+       700   0.07           0.093779218   -3.3532704     -3.3532704      0             -3.3532704    
+       800   0.08           0.097960251   -3.9343481     -3.9343481      0             -3.9343481    
+       900   0.09           0.10193598    -4.7944099     -4.7944099      0             -4.7944099    
+      1000   0.1            0.10832963    -5.3823924     -5.3823924      0             -5.3823924    
+Loop time of 0.40066 on 4 procs for 1000 steps with 500 atoms
+
+Performance: 21.564 ns/day, 1.113 hours/ns, 2495.885 timesteps/s, 1.248 Matom-step/s
+97.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.032435   | 0.033013   | 0.033957   |   0.3 |  8.24
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.016106   | 0.016898   | 0.017915   |   0.5 |  4.22
+Output  | 0.00012331 | 0.00013523 | 0.00016852 |   0.0 |  0.03
+Modify  | 0.34913    | 0.34974    | 0.35017    |   0.1 | 87.29
+Other   |            | 0.0008755  |            |       |  0.22
+
+Nlocal:            125 ave         125 max         125 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:          597.5 ave         600 max         595 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:              0 ave           0 max           0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:         2500 ave        2500 max        2500 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 10000
+Ave neighs/atom = 20
+Neighbor list builds = 0
+Dangerous builds = 0
+write_restart   restart_hcp_cobalt.equil
+System init for write_restart ...
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Total wall time: 0:00:00

examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.1

@@ -1,110 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-dimension 	3
-boundary 	p p p
-
-atom_style 	spin
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-read_data 	Norm_randXY_8x8x32.data
-  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  8192 atoms
-  read_data CPU = 0.022048 secs
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs and computes
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 8 8 31
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 19.99 | 19.99 | 19.99 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-       0                    0   0.0177864461018737    -36558.7284872918    -661.829206399896       1274.398774669                    0    -36558.7284872918 
-      20                0.002   0.0177864377256184    -36558.7389378387    -661.839683504936     1259.94171978912  0.00986992693139795    -36558.7284878577 
-      40                0.004    0.017786472977471    -36558.7684525639    -661.869582914286     1224.05894016152   0.0377451568363827    -36558.7284891299 
-      60                0.006   0.0177865119543331    -36558.8126238543    -661.915330492427     1184.24369688088   0.0794631076347515     -36558.728490712 
-      80                0.008   0.0177865172048059    -36558.8659242367    -661.972562482488     1152.05459929593    0.129803482511904    -36558.7284922233 
-     100                 0.01   0.0177865063752424    -36558.9229549739    -662.037138807935     1129.51470280479    0.183667498513087    -36558.7284933644 
-Loop time of 14.3276 on 1 procs for 100 steps with 8192 atoms
-
-Performance: 0.060 ns/day, 397.988 hours/ns, 6.980 timesteps/s
-99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 4.0409     | 4.0409     | 4.0409     |   0.0 | 28.20
-Neigh   | 3.6219     | 3.6219     | 3.6219     |   0.0 | 25.28
-Comm    | 0.055327   | 0.055327   | 0.055327   |   0.0 |  0.39
-Output  | 2.4259     | 2.4259     | 2.4259     |   0.0 | 16.93
-Modify  | 4.1688     | 4.1688     | 4.1688     |   0.0 | 29.10
-Other   |            | 0.01477    |            |       |  0.10
-
-Nlocal:    8192 ave 8192 max 8192 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    14621 ave 14621 max 14621 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    573440 ave 573440 max 573440 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  1.14688e+06 ave 1.14688e+06 max 1.14688e+06 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 1146880
-Ave neighs/atom = 140
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:14

examples/SPIN/read_restart/log.14Apr20.spin.read_data.g++.4

@@ -1,110 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-units 		metal
-dimension 	3
-boundary 	p p p
-
-atom_style 	spin
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-read_data 	Norm_randXY_8x8x32.data
-  orthogonal box = (0 0 0) to (28.32 28.32 113.28)
-  1 by 1 by 4 MPI processor grid
-  reading atoms ...
-  8192 atoms
-  read_data CPU = 0.013634 secs
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.0446928 0.003496 1.4885
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs and computes
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		1 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 8 8 31
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 8.961 | 9.047 | 9.29 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-       0                    0   0.0177864461018739    -36558.7284872997    -661.829206399894       1274.398774669                    0    -36558.7284872997 
-      20                0.002   0.0177863981273124    -36558.7389378386    -661.839683504262     1259.94177798388  0.00986992629371963    -36558.7284878582 
-      40                0.004   0.0177864622701489    -36558.7684525586    -661.869582908114     1224.05908191331   0.0377451510479599    -36558.7284891308 
-      60                0.006   0.0177865625037858    -36558.8126238326    -661.915330472361     1184.24389640891   0.0794630890177406      -36558.72849071 
-      80                0.008   0.0177865898045059    -36558.8659241943    -661.972562439245     1152.05483020781    0.129803443061299    -36558.7284922226 
-     100                 0.01    0.017786565190115    -36558.9229549058    -662.037138735432     1129.51495182843    0.183667434061771    -36558.7284933646 
-Loop time of 4.35911 on 4 procs for 100 steps with 8192 atoms
-
-Performance: 0.198 ns/day, 121.086 hours/ns, 22.940 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 1.0924     | 1.1043     | 1.1117     |   0.7 | 25.33
-Neigh   | 0.93575    | 0.94926    | 0.98325    |   2.0 | 21.78
-Comm    | 0.044663   | 0.088288   | 0.11128    |   8.7 |  2.03
-Output  | 0.64199    | 0.6587     | 0.67226    |   1.4 | 15.11
-Modify  | 1.5412     | 1.5535     | 1.5706     |   0.9 | 35.64
-Other   |            | 0.005046   |            |       |  0.12
-
-Nlocal:    2048 ave 2061 max 2035 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Nghost:    5765 ave 5778 max 5752 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-Neighs:    143360 ave 144262 max 142469 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-FullNghs:  286720 ave 288540 max 284900 min
-Histogram: 1 0 0 1 0 0 1 0 0 1
-
-Total # of neighbors = 1146880
-Ave neighs/atom = 140
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:04

examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.1

@@ -1,116 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# start a spin-lattice simulation from a data file
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-read_restart	restart_hcp_cobalt.equil
-WARNING: Restart file used different # of processors: 4 vs. 1 (../read_restart.cpp:736)
-  restoring atom style spin from restart
-  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 1 by 1 MPI processor grid
-  restoring pair style spin/exchange from restart
-  500 atoms
-  read_restart CPU = 0.00179696 secs
-
-# setting mass, mag. moments, and interactions
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 4 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.422 | 7.422 | 7.422 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-    1000                    0    0.108317262557656    -2200.38241212222    -5.38245988668244      2538.4247868621                    0    -2200.38241212222 
-    1020                0.002    0.108317318495042    -2200.39172132133    -5.39179331134703     2513.42968070374    0.144319963844279    -2200.38241256643 
-    1040                0.004    0.108317415558744    -2200.41811580407      -5.418541526637     2478.87571728648    0.553516420254567    -2200.38241354532 
-    1060                0.006    0.108317473592946    -2200.45801216332    -5.45990062771403     2449.77257658726     1.17203792179707    -2200.38241476526 
-    1080                0.008    0.108317450745396     -2200.5068824087    -5.51245983698347     2427.25022669715     1.92968606059505     -2200.3824160902 
-    1100                 0.01    0.108317381572202    -2200.55976028827    -5.57250071024394     2400.86131889957     2.74946927499959    -2200.38241728649 
-Loop time of 0.954493 on 1 procs for 100 steps with 500 atoms
-
-Performance: 0.905 ns/day, 26.514 hours/ns, 104.768 timesteps/s
-100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.27043    | 0.27043    | 0.27043    |   0.0 | 28.33
-Neigh   | 0.26148    | 0.26148    | 0.26148    |   0.0 | 27.40
-Comm    | 0.0071123  | 0.0071123  | 0.0071123  |   0.0 |  0.75
-Output  | 0.14169    | 0.14169    | 0.14169    |   0.0 | 14.84
-Modify  | 0.2726     | 0.2726     | 0.2726     |   0.0 | 28.56
-Other   |            | 0.001178   |            |       |  0.12
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2534 ave 2534 max 2534 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    36500 ave 36500 max 36500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  73000 ave 73000 max 73000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 73000
-Ave neighs/atom = 146
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01

examples/SPIN/read_restart/log.14Apr20.spin.restart.g++.4

@@ -1,115 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# start a spin-lattice simulation from a data file
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary 	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-read_restart	restart_hcp_cobalt.equil
-  restoring atom style spin from restart
-  orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-  restoring pair style spin/exchange from restart
-  500 atoms
-  read_restart CPU = 0.00173593 secs
-
-# setting mass, mag. moments, and interactions
-
-mass		1 58.93
-
-pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0
-pair_coeff 	* * eam/alloy Co_PurjaPun_2012.eam.alloy Co
-pair_coeff 	* * spin/exchange exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	1.0 bin
-neigh_modify 	every 1 check no delay 0
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 0.0 0.0 21
-
-fix 		3 all nve/spin lattice moving
-timestep	0.0001
-
-# define outputs
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo          20
-thermo_style    custom step time v_magnorm pe v_emag v_tmag temp etotal
-thermo_modify   format float %20.15g
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		100
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check no
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 7.49954
-  ghost atom cutoff = 7.49954
-  binsize = 3.74977, bins = 4 6 6
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair eam/alloy, perpetual, half/full from (2)
-      attributes: half, newton on
-      pair build: halffull/newton
-      stencil: none
-      bin: none
-  (2) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 7.324 | 7.324 | 7.324 Mbytes
-Step Time v_magnorm PotEng v_emag v_tmag Temp TotEng 
-    1000                    0    0.108317262557656    -2200.38241212182    -5.38245988668244      2538.4247868621                    0    -2200.38241212182 
-    1020                0.002    0.108317316216432    -2200.39172132147    -5.39179331147409     2513.42945241007     0.14431996581917    -2200.38241256644 
-    1040                0.004    0.108317347939802    -2200.41811580574    -5.41854152831072     2478.87544274124    0.553516446104432    -2200.38241354532 
-    1060                0.006    0.108317342440309    -2200.45801216927    -5.45990063373049     2449.77218633122     1.17203801398165    -2200.38241476526 
-    1080                0.008    0.108317320345284    -2200.50688241767    -5.51245984623572      2427.2497145488     1.92968619968329     -2200.3824160902 
-    1100                 0.01     0.10831728372281    -2200.55976028296    -5.57250070536486     2400.86059511731     2.74946919265255    -2200.38241728649 
-Loop time of 0.405615 on 4 procs for 100 steps with 500 atoms
-
-Performance: 2.130 ns/day, 11.267 hours/ns, 246.539 timesteps/s
-99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.075661   | 0.076798   | 0.077343   |   0.2 | 18.93
-Neigh   | 0.063154   | 0.064974   | 0.066991   |   0.5 | 16.02
-Comm    | 0.012538   | 0.013787   | 0.015151   |   0.8 |  3.40
-Output  | 0.039155   | 0.040842   | 0.042502   |   0.6 | 10.07
-Modify  | 0.20709    | 0.20883    | 0.21036    |   0.3 | 51.49
-Other   |            | 0.0003826  |            |       |  0.09
-
-Nlocal:    125 ave 127 max 122 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-Nghost:    1387 ave 1390 max 1385 min
-Histogram: 2 0 0 0 0 0 1 0 0 1
-Neighs:    9125 ave 9272 max 8945 min
-Histogram: 1 0 0 1 0 0 0 0 1 1
-FullNghs:  18250 ave 18542 max 17812 min
-Histogram: 1 0 0 0 1 0 0 0 0 2
-
-Total # of neighbors = 73000
-Ave neighs/atom = 146
-Neighbor list builds = 100
-Dangerous builds not checked
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:00

examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.1

@@ -1,120 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# fcc cobalt in a 3d periodic box
-
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 1 by 1 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000952005 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.93
-
-set 		group all spin/random 31 1.72
-  500 settings made for spin/random
-
-pair_style	spin/exchange 4.0
-pair_coeff 	* * exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 100.0 0.01 21
-
-fix 		3 all nve/spin lattice frozen
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm pe v_emag temp etotal
-thermo          100
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 4.1
-  ghost atom cutoff = 4.1
-  binsize = 2.05, bins = 7 11 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.947 | 6.947 | 6.947 Mbytes
-Step Time v_magnorm PotEng v_emag Temp TotEng 
-       0            0  0.076558814   0.89911794   0.89911794            0   0.89911794 
-     100         0.01  0.077628154   0.36693917   0.36693917            0   0.36693917 
-     200         0.02  0.076678996  -0.20242315  -0.20242315            0  -0.20242315 
-     300         0.03  0.079174837  -0.67595514  -0.67595514            0  -0.67595514 
-     400         0.04  0.085031632   -1.5172851   -1.5172851            0   -1.5172851 
-     500         0.05   0.08702747   -2.0426628   -2.0426628            0   -2.0426628 
-     600         0.06  0.087066482   -2.6297745   -2.6297745            0   -2.6297745 
-     700         0.07  0.089788894    -3.314538    -3.314538            0    -3.314538 
-     800         0.08  0.091699611   -4.0287043   -4.0287043            0   -4.0287043 
-     900         0.09  0.090038899    -4.600601    -4.600601            0    -4.600601 
-    1000          0.1  0.093257309   -5.2352261   -5.2352261            0   -5.2352261 
-Loop time of 3.30071 on 1 procs for 1000 steps with 500 atoms
-
-Performance: 2.618 ns/day, 9.169 hours/ns, 302.965 timesteps/s
-99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.3844     | 0.3844     | 0.3844     |   0.0 | 11.65
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.019863   | 0.019863   | 0.019863   |   0.0 |  0.60
-Output  | 1.3844     | 1.3844     | 1.3844     |   0.0 | 41.94
-Modify  | 1.5084     | 1.5084     | 1.5084     |   0.0 | 45.70
-Other   |            | 0.00367    |            |       |  0.11
-
-Nlocal:    500 ave 500 max 500 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    1221 ave 1221 max 1221 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-FullNghs:  10000 ave 10000 max 10000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 10000
-Ave neighs/atom = 20
-Neighbor list builds = 0
-Dangerous builds = 0
-write_restart 	restart_hcp_cobalt.equil
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:03

examples/SPIN/read_restart/log.14Apr20.spin.write_restart.g++.4

@@ -1,120 +0,0 @@
-LAMMPS (19 Mar 2020)
-OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:94)
-  using 1 OpenMP thread(s) per MPI task
-# fcc cobalt in a 3d periodic box
-
-units 		metal
-atom_style 	spin
-
-dimension 	3
-boundary	p p p
-
-# necessary for the serial algorithm (sametag)
-atom_modify 	map array
-
-lattice 	hcp 2.5071
-Lattice spacing in x,y,z = 2.5071 4.34242 4.09408
-region 		box block 0.0 5.0 0.0 5.0 0.0 5.0
-create_box 	1 box
-Created orthogonal box = (0 0 0) to (12.5355 21.7121 20.4704)
-  1 by 2 by 2 MPI processor grid
-create_atoms 	1 box
-Created 500 atoms
-  create_atoms CPU = 0.000663042 secs
-
-# setting mass, mag. moments, and interactions for cobalt
-
-mass		1 58.93
-
-set 		group all spin/random 31 1.72
-  500 settings made for spin/random
-
-pair_style	spin/exchange 4.0
-pair_coeff 	* * exchange 4.0 0.3593 1.135028015e-05 1.064568567
-
-neighbor 	0.1 bin
-neigh_modify 	every 10 check yes delay 20
-
-fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix 		2 all langevin/spin 100.0 0.01 21
-
-fix 		3 all nve/spin lattice frozen
-timestep	0.0001
-
-# compute and output options
-
-compute 	out_mag    all spin
-compute 	out_pe     all pe
-compute 	out_ke     all ke
-compute 	out_temp   all temp
-
-variable 	magz      equal c_out_mag[3]
-variable 	magnorm   equal c_out_mag[4]
-variable 	emag      equal c_out_mag[5]
-variable 	tmag      equal c_out_mag[6]
-
-thermo_style    custom step time v_magnorm pe v_emag temp etotal
-thermo          100
-
-compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
-dump 		100 all custom 1 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7]
-
-run 		1000
-Neighbor list info ...
-  update every 10 steps, delay 20 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 4.1
-  ghost atom cutoff = 4.1
-  binsize = 2.05, bins = 7 11 10
-  1 neighbor lists, perpetual/occasional/extra = 1 0 0
-  (1) pair spin/exchange, perpetual
-      attributes: full, newton on
-      pair build: full/bin/atomonly
-      stencil: full/bin/3d
-      bin: standard
-Per MPI rank memory allocation (min/avg/max) = 6.868 | 6.868 | 6.868 Mbytes
-Step Time v_magnorm PotEng v_emag Temp TotEng 
-       0            0  0.076558814   0.89911794   0.89911794            0   0.89911794 
-     100         0.01  0.078299981   0.44129792   0.44129792            0   0.44129792 
-     200         0.02  0.081260508  -0.21742361  -0.21742361            0  -0.21742361 
-     300         0.03  0.081195603  -0.87041046  -0.87041046            0  -0.87041046 
-     400         0.04  0.087298495   -1.7069519   -1.7069519            0   -1.7069519 
-     500         0.05  0.087663924   -2.1883045   -2.1883045            0   -2.1883045 
-     600         0.06  0.091713683   -2.9267461   -2.9267461            0   -2.9267461 
-     700         0.07  0.093779119    -3.353314    -3.353314            0    -3.353314 
-     800         0.08  0.097960611   -3.9344284   -3.9344284            0   -3.9344284 
-     900         0.09   0.10193463   -4.7944004   -4.7944004            0   -4.7944004 
-    1000          0.1   0.10831726   -5.3824599   -5.3824599            0   -5.3824599 
-Loop time of 1.7839 on 4 procs for 1000 steps with 500 atoms
-
-Performance: 4.843 ns/day, 4.955 hours/ns, 560.569 timesteps/s
-99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.10068    | 0.10749    | 0.11461    |   1.5 |  6.03
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0.052378   | 0.062171   | 0.07177    |   2.8 |  3.49
-Output  | 0.4054     | 0.42334    | 0.44025    |   2.0 | 23.73
-Modify  | 1.174      | 1.1893     | 1.2043     |   1.1 | 66.67
-Other   |            | 0.001558   |            |       |  0.09
-
-Nlocal:    125 ave 125 max 125 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    597.5 ave 600 max 595 min
-Histogram: 2 0 0 0 0 0 0 0 0 2
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-FullNghs:  2500 ave 2500 max 2500 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 10000
-Ave neighs/atom = 20
-Neighbor list builds = 0
-Dangerous builds = 0
-write_restart 	restart_hcp_cobalt.equil
-
-Please see the log.cite file for references relevant to this simulation
-
-Total wall time: 0:00:01

examples/SPIN/test_problems/validation_nve/in.spin.iron-nve

@@ -50,5 +50,5 @@ thermo          200
 compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
 dump 		1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
 
-run 		100000
+run 		10000
 # run 		1

examples/SPIN/test_problems/validation_nve/log.11Mar25.spin.iron-nve.g++.1

@@ -0,0 +1,188 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# bcc iron in a 3d periodic box
+
+clear
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units 		metal
+atom_style 	spin
+# atom_style 	spin/kk
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 3.0 0.0 3.0 0.0 3.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 54 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
+  create_atoms CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin/random 31 2.2
+Setting atom values ...
+WARNING: Set attribute spin/random is deprecated. Please use spin/atom/random instead. (src/set.cpp:293)
+  54 settings made for spin/random
+velocity 	all create 100 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.02726 0.2171 1.841
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix 		2 all langevin/spin 0.0 0.00 21
+fix 		3 all nve/spin lattice moving
+timestep	0.0001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_tmag temp v_emag ke pe etotal
+thermo          200
+
+compute 	outsp all property/atom spx spy spz sp fmx fmy fmz
+dump 		1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3]
+
+run 		10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.773367
+  ghost atom cutoff = 5.773367
+  binsize = 2.8866835, bins = 3 3 3
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 5.7733670002446
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+WARNING: Dump 1 includes no atom IDs and is not sorted by ID. This may complicate post-processing tasks or visualization (src/dump.cpp:220)
+Per MPI rank memory allocation (min/avg/max) = 5.626 | 5.626 | 5.626 Mbytes
+   Step          Time          v_tmag          Temp          v_emag         KinEng         PotEng         TotEng    
+         0   0              1836.2373      100.00358     -0.26674297     0.6851033     -231.38675     -230.70164    
+       200   0.02           1751.0384      48.019015     -0.27512361     0.32896808    -231.03061     -230.70164    
+       400   0.04           1776.2639      19.035769     -0.28188188     0.13041001    -230.83205     -230.70164    
+       600   0.06           1787.5802      60.069761     -0.2772323      0.41152518    -231.11317     -230.70164    
+       800   0.08           1706.5552      50.79606      -0.27292548     0.34799302    -231.04963     -230.70164    
+      1000   0.1            2120.1611      44.605193     -0.26987056     0.3055807     -231.00722     -230.70164    
+      1200   0.12           1754.9393      64.57232      -0.26943293     0.44237126    -231.14401     -230.70164    
+      1400   0.14           1912.6009      44.177766     -0.26857448     0.3026525     -231.00429     -230.70164    
+      1600   0.16           1875.5315      40.249733     -0.27481087     0.27574238    -230.97738     -230.70164    
+      1800   0.18           1837.1786      62.817536     -0.28092582     0.4303496     -231.13199     -230.70164    
+      2000   0.2            1860.1719      54.167659     -0.28282659     0.37109113    -231.07273     -230.70164    
+      2200   0.22           1691.658       46.643932     -0.29528237     0.31954767    -231.02119     -230.70164    
+      2400   0.24           1525.2579      57.361866     -0.30189945     0.39297397    -231.09462     -230.70164    
+      2600   0.26           1505.1726      56.239347     -0.30898994     0.38528383    -231.08693     -230.70164    
+      2800   0.28           1415.9555      47.818074     -0.31351411     0.32759147    -231.02923     -230.70164    
+      3000   0.3            1248.4308      49.608492     -0.31727375     0.33985725    -231.0415      -230.70164    
+      3200   0.32           1200.7605      51.495405     -0.31565357     0.35278409    -231.05443     -230.70164    
+      3400   0.34           1746.137       56.967184     -0.30906485     0.39027008    -231.09191     -230.70164    
+      3600   0.36           1805.3667      55.030692     -0.30799197     0.37700359    -231.07865     -230.70164    
+      3800   0.38           1609.9498      59.452017     -0.30520539     0.40729315    -231.10894     -230.70164    
+      4000   0.4            1686.1863      57.338707     -0.30240026     0.39281531    -231.09446     -230.70164    
+      4200   0.42           1961.3516      41.421108     -0.30479326     0.28376722    -230.98541     -230.70164    
+      4400   0.44           1971.1808      54.038289     -0.30876936     0.37020484    -231.07185     -230.70164    
+      4600   0.46           1819.428       56.766201     -0.3129157      0.38889319    -231.09054     -230.70164    
+      4800   0.48           1494.1263      47.402453     -0.32868332     0.32474414    -231.02639     -230.70164    
+      5000   0.5            1601.6127      63.404101     -0.33283819     0.43436803    -231.13601     -230.70164    
+      5200   0.52           1567.7429      62.783792     -0.34753005     0.43011843    -231.13176     -230.70164    
+      5400   0.54           1686.234       40.450417     -0.3603489      0.27711722    -230.97876     -230.70164    
+      5600   0.56           1651.1927      64.255456     -0.36569031     0.44020049    -231.14184     -230.70164    
+      5800   0.58           1380.639       75.386226     -0.36870019     0.51645503    -231.2181      -230.70164    
+      6000   0.6            1539.07        40.611642     -0.36303517     0.27822173    -230.97986     -230.70164    
+      6200   0.62           1442.2286      50.254503     -0.36560331     0.34428293    -231.04592     -230.70164    
+      6400   0.64           1263.6928      69.095161     -0.36822748     0.47335628    -231.175       -230.70164    
+      6600   0.66           1468.1529      54.534243     -0.37319988     0.37360252    -231.07524     -230.70164    
+      6800   0.68           1289.4927      60.381892     -0.38478834     0.41366352    -231.11531     -230.70164    
+      7000   0.7            1121.6702      58.691171     -0.39652609     0.40208075    -231.10372     -230.70164    
+      7200   0.72           1018.1068      53.528417     -0.40711639     0.36671182    -231.06835     -230.70164    
+      7400   0.74           1115.0342      78.62129      -0.41729373     0.53861776    -231.24026     -230.70164    
+      7600   0.76           1329.4621      65.650574     -0.41928751     0.44975815    -231.1514      -230.70164    
+      7800   0.78           1154.164       45.603278     -0.41263444     0.31241837    -231.01406     -230.70164    
+      8000   0.8            1090.2959      62.148282     -0.40987933     0.42576469    -231.12741     -230.70164    
+      8200   0.82           1303.4698      63.864431     -0.41301445     0.43752166    -231.13916     -230.70164    
+      8400   0.84           1144.2181      52.222297     -0.41645089     0.35776387    -231.05941     -230.70164    
+      8600   0.86           1005.3359      61.59129      -0.41282114     0.42194885    -231.12359     -230.70164    
+      8800   0.88           1453.8465      70.876149     -0.41920851     0.48555745    -231.1872      -230.70164    
+      9000   0.9            1325.9116      63.675151     -0.42450864     0.43622494    -231.13787     -230.70164    
+      9200   0.92           1213.5738      58.297881     -0.42722791     0.3993864     -231.10103     -230.70164    
+      9400   0.94           1227.437       57.375795     -0.44309693     0.39306939    -231.09471     -230.70164    
+      9600   0.96           1192.79        65.822598     -0.44760999     0.45093664    -231.15258     -230.70164    
+      9800   0.98           1231.5166      69.119896     -0.45335245     0.47352573    -231.17517     -230.70164    
+     10000   1              1284.2809      66.166068     -0.45872955     0.45328969    -231.15493     -230.70164    
+Loop time of 5.97474 on 1 procs for 10000 steps with 54 atoms
+
+Performance: 14.461 ns/day, 1.660 hours/ns, 1673.714 timesteps/s, 90.381 katom-step/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.501      | 2.501      | 2.501      |   0.0 | 41.86
+Neigh   | 0.016481   | 0.016481   | 0.016481   |   0.0 |  0.28
+Comm    | 0.37576    | 0.37576    | 0.37576    |   0.0 |  6.29
+Output  | 0.12311    | 0.12311    | 0.12311    |   0.0 |  2.06
+Modify  | 2.9317     | 2.9317     | 2.9317     |   0.0 | 49.07
+Other   |            | 0.02661    |            |       |  0.45
+
+Nlocal:             54 ave          54 max          54 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            777 ave         777 max         777 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1700 ave        1700 max        1700 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:         3400 ave        3400 max        3400 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3400
+Ave neighs/atom = 62.962963
+Neighbor list builds = 58
+Dangerous builds = 0
+# run 		1
+Total wall time: 0:00:06

examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice

@@ -49,4 +49,4 @@ variable 	tmag      equal c_out_mag[6]
 thermo_style    custom step time v_tmag temp v_emag ke pe etotal
 thermo          200
 
-run 		200000
+run 		20000

examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin

@@ -32,7 +32,7 @@ neighbor 	0.1 bin
 neigh_modify 	every 10 check yes delay 20
 
 fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
-fix             2 all langevin 0.0 0.0 0.0 48279
+fix         2 all langevin 0.0 0.0 0.001 48279
 fix 		3 all langevin/spin 200.0 0.01 321
 fix 		4 all nve/spin lattice moving
 timestep	0.001
@@ -50,4 +50,4 @@ variable 	tmag      equal c_out_mag[6]
 thermo_style    custom step time v_tmag temp v_emag ke pe etotal
 thermo          200
 
-run 		200000
+run 		20000

examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_lattice.g++.1

@@ -0,0 +1,240 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# bcc iron in a 3d periodic box
+
+clear
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units 		metal
+atom_style 	spin
+# atom_style 	spin/kk
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 3.0 0.0 3.0 0.0 3.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 54 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
+  create_atoms CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 0.0 0.0 1.0
+Setting atom values ...
+WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268)
+  54 settings made for spin
+velocity 	all create 400 4928459 rot yes dist gaussian
+
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.1 0.2171 1.841
+pair_coeff 	* * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix             2 all langevin 200.0 200.0 0.1 48279
+fix 		3 all langevin/spin 0.0 0.0 321
+fix 		4 all nve/spin lattice moving
+timestep	0.001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_tmag temp v_emag ke pe etotal
+thermo          200
+
+run 		20000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.773367
+  ghost atom cutoff = 5.773367
+  binsize = 2.8866835, bins = 3 3 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 5.7733670002446
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/neel, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes
+   Step          Time          v_tmag          Temp          v_emag         KinEng         PotEng         TotEng    
+         0   0              1.4336203e-31  400.01433     -22.021022      2.7404132     -253.14103     -250.40061    
+       200   0.2            0.26275543     188.91786     -21.983513      1.2942362     -251.94911     -250.65488    
+       400   0.4            0.56095049     204.95947     -21.977046      1.4041338     -251.914       -250.50987    
+       600   0.6            0.81480981     203.28763     -21.98548       1.3926804     -251.88478     -250.4921     
+       800   0.8            0.97590428     184.8694      -21.974142      1.266501      -251.73716     -250.47066    
+      1000   1              1.1324742      184.65547     -21.986309      1.2650354     -252.03248     -250.76744    
+      1200   1.2            1.5284342      207.55788     -21.974821      1.421935      -251.7769      -250.35497    
+      1400   1.4            1.8310776      220.75396     -21.979994      1.5123385     -251.93989     -250.42755    
+      1600   1.6            2.2057174      236.04272     -21.973951      1.6170785     -251.98625     -250.36917    
+      1800   1.8            2.7760928      195.92697     -21.96808       1.3422541     -251.7495      -250.40725    
+      2000   2              3.2171354      161.33811     -21.975129      1.1052932     -251.86337     -250.75808    
+      2200   2.2            3.8284998      193.21861     -21.968067      1.3236997     -251.86609     -250.54239    
+      2400   2.4            4.4109629      203.79368     -21.971813      1.3961472     -251.92264     -250.52649    
+      2600   2.6            4.5056291      200.81431     -21.960649      1.3757362     -251.80976     -250.43403    
+      2800   2.8            4.6221125      185.57027     -21.972664      1.2713025     -252.0384      -250.76709    
+      3000   3              4.9059897      216.00877     -21.966875      1.4798302     -252.13406     -250.65423    
+      3200   3.2            5.3958965      152.77626     -21.956779      1.0466377     -251.66        -250.61337    
+      3400   3.4            5.9881406      170.70538     -21.964189      1.1694663     -251.9061      -250.73663    
+      3600   3.6            6.134982       210.99981     -21.945137      1.4455149     -251.75025     -250.30474    
+      3800   3.8            6.5940545      239.12527     -21.953159      1.6381964     -251.90813     -250.26993    
+      4000   4              6.9355034      181.99614     -21.938591      1.2468169     -251.59724     -250.35043    
+      4200   4.2            7.3712919      242.52183     -21.932318      1.6614656     -251.71104     -250.04957    
+      4400   4.4            7.5924709      164.34328     -21.942361      1.1258809     -251.64032     -250.51444    
+      4600   4.6            8.1833481      205.94973     -21.941491      1.4109179     -251.57627     -250.16536    
+      4800   4.8            8.40416        169.96914     -21.945774      1.1644225     -251.87887     -250.71444    
+      5000   5              8.4422416      189.79518     -21.94955       1.3002465     -251.80055     -250.50031    
+      5200   5.2            8.3667008      195.86473     -21.934302      1.3418277     -251.64678     -250.30495    
+      5400   5.4            8.7075519      204.82319     -21.947339      1.4032002     -251.85712     -250.45392    
+      5600   5.6            8.6582399      191.25854     -21.933614      1.3102717     -251.51648     -250.2062     
+      5800   5.8            8.896287       180.44446     -21.923523      1.2361867     -251.68003     -250.44384    
+      6000   6              9.1379808      248.49596     -21.938845      1.7023931     -251.84502     -250.14263    
+      6200   6.2            8.9724294      181.67979     -21.939567      1.2446497     -251.81639     -250.57174    
+      6400   6.4            8.7735241      198.31668     -21.952115      1.3586255     -251.97841     -250.61979    
+      6600   6.6            9.0394523      218.6735      -21.934717      1.4980857     -251.85133     -250.35325    
+      6800   6.8            9.5779186      203.83536     -21.937873      1.3964328     -251.98448     -250.58804    
+      7000   7              9.7893273      185.56096     -21.949319      1.2712387     -252.09057     -250.81934    
+      7200   7.2            9.5292481      205.53224     -21.936466      1.4080577     -251.98037     -250.57231    
+      7400   7.4            9.7369072      200.76528     -21.944609      1.3754003     -251.88128     -250.50588    
+      7600   7.6            9.9385522      217.68239     -21.920768      1.4912959     -251.6169      -250.1256     
+      7800   7.8            9.8656638      219.17274     -21.92302       1.5015059     -251.50189     -250.00039    
+      8000   8              9.2380618      264.13229     -21.936112      1.8095143     -251.71532     -249.9058     
+      8200   8.2            9.3384949      239.58029     -21.941834      1.6413137     -251.73551     -250.0942     
+      8400   8.4            9.1684312      207.27974     -21.938426      1.4200295     -251.59062     -250.17059    
+      8600   8.6            8.8407032      200.79452     -21.933328      1.3756006     -251.48006     -250.10446    
+      8800   8.8            8.84683        218.44316     -21.949738      1.4965077     -251.92925     -250.43275    
+      9000   9              9.0686442      216.06373     -21.942255      1.4802067     -251.79797     -250.31776    
+      9200   9.2            9.2783597      187.56662     -21.93374       1.2849791     -251.87884     -250.59386    
+      9400   9.4            9.2794158      203.78139     -21.955284      1.396063      -252.09328     -250.69722    
+      9600   9.6            9.3563189      196.15871     -21.948544      1.3438417     -251.85685     -250.51301    
+      9800   9.8            9.6458819      215.38334     -21.94895       1.4755455     -251.92219     -250.44665    
+     10000   10             9.5073837      178.61601     -21.955281      1.2236604     -251.97306     -250.7494     
+     10200   10.2           9.3510908      185.21136     -21.94749       1.2688437     -251.83233     -250.56349    
+     10400   10.4           9.8171891      194.92192     -21.945394      1.3353687     -251.86067     -250.5253     
+     10600   10.6           9.5996138      213.90302     -21.945461      1.4654042     -251.72508     -250.25968    
+     10800   10.8           9.8602813      208.57912     -21.936736      1.4289312     -251.55778     -250.12885    
+     11000   11             10.652287      202.88507     -21.933085      1.3899225     -251.69631     -250.30639    
+     11200   11.2           10.413298      171.86972     -21.919711      1.1774429     -251.16232     -249.98488    
+     11400   11.4           10.589727      179.33897     -21.927537      1.2286132     -251.65266     -250.42405    
+     11600   11.6           11.099271      176.43012     -21.925025      1.2086853     -251.65796     -250.44927    
+     11800   11.8           11.49558       216.78529     -21.935923      1.48515       -251.51958     -250.03443    
+     12000   12             11.190687      206.45545     -21.941866      1.4143824     -251.55494     -250.14055    
+     12200   12.2           11.372777      216.26373     -21.934028      1.4815769     -251.75482     -250.27324    
+     12400   12.4           11.303952      218.67625     -21.928577      1.4981046     -251.73908     -250.24098    
+     12600   12.6           11.065605      188.25083     -21.925979      1.2896665     -251.49808     -250.20841    
+     12800   12.8           11.289265      209.423       -21.933529      1.4347125     -251.85142     -250.41671    
+     13000   13             11.412931      148.86392     -21.93732       1.0198351     -251.88347     -250.86364    
+     13200   13.2           11.677538      187.03356     -21.923919      1.2813272     -251.52124     -250.23991    
+     13400   13.4           12.451801      237.44268     -21.93385       1.6266694     -251.70112     -250.07445    
+     13600   13.6           12.981208      196.47947     -21.926751      1.3460391     -251.80509     -250.45905    
+     13800   13.8           13.301789      191.61721     -21.921891      1.3127288     -251.85541     -250.54268    
+     14000   14             13.726635      212.61693     -21.922086      1.4565934     -252.06804     -250.61145    
+     14200   14.2           13.715662      197.51397     -21.915949      1.3531263     -251.71314     -250.36002    
+     14400   14.4           13.340257      210.15601     -21.927197      1.4397342     -251.73271     -250.29297    
+     14600   14.6           14.118672      175.1782      -21.923635      1.2001087     -251.54286     -250.34275    
+     14800   14.8           14.52801       211.5541      -21.919371      1.4493122     -251.74119     -250.29188    
+     15000   15             14.522566      207.59406     -21.919623      1.4221828     -251.74192     -250.31974    
+     15200   15.2           15.1446        191.32404     -21.902291      1.3107204     -251.52754     -250.21682    
+     15400   15.4           15.815481      160.35385     -21.918453      1.0985502     -251.75506     -250.65651    
+     15600   15.6           16.942896      211.32891     -21.89554       1.4477695     -251.42064     -249.97287    
+     15800   15.8           17.339057      213.03178     -21.903747      1.4594355     -251.5815      -250.12207    
+     16000   16             17.610695      211.72009     -21.899083      1.4504494     -251.51043     -250.05998    
+     16200   16.2           18.352293      236.99887     -21.9043        1.623629      -251.79466     -250.17103    
+     16400   16.4           17.898896      208.62272     -21.904247      1.42923       -251.66653     -250.2373     
+     16600   16.6           18.005606      169.07581     -21.910252      1.1583025     -251.84184     -250.68353    
+     16800   16.8           18.884686      198.75251     -21.900417      1.3616113     -251.8573      -250.49569    
+     17000   17             19.454235      182.70172     -21.904544      1.2516507     -251.66187     -250.41021    
+     17200   17.2           19.497759      157.47203     -21.904461      1.0788075     -251.88582     -250.80701    
+     17400   17.4           19.470705      215.43531     -21.887158      1.4759016     -251.82426     -250.34836    
+     17600   17.6           19.553888      212.82066     -21.89372       1.4579892     -251.79955     -250.34157    
+     17800   17.8           19.646117      236.85339     -21.8983        1.6226323     -251.75304     -250.13041    
+     18000   18             20.205554      253.85283     -21.909061      1.7390919     -251.84228     -250.10319    
+     18200   18.2           20.065135      233.11058     -21.882631      1.5969911     -251.54972     -249.95273    
+     18400   18.4           20.76763       209.7018      -21.895306      1.4366225     -251.79971     -250.36309    
+     18600   18.6           21.369833      214.39422     -21.882332      1.4687693     -251.53344     -250.06467    
+     18800   18.8           21.939164      216.25928     -21.89097       1.4815464     -251.82112     -250.33958    
+     19000   19             22.817363      215.27695     -21.882698      1.4748166     -251.82572     -250.3509     
+     19200   19.2           23.705114      182.22745     -21.879076      1.2484016     -251.43044     -250.18204    
+     19400   19.4           23.441248      222.83743     -21.879144      1.5266119     -251.76376     -250.23715    
+     19600   19.6           23.435558      218.16026     -21.86114       1.4945696     -251.59729     -250.10272    
+     19800   19.8           24.074607      222.78958     -21.87264       1.5262841     -251.7863      -250.26001    
+     20000   20             23.618814      222.44332     -21.870985      1.5239119     -251.37299     -249.84908    
+Loop time of 22.6158 on 1 procs for 20000 steps with 54 atoms
+
+Performance: 76.407 ns/day, 0.314 hours/ns, 884.338 timesteps/s, 47.754 katom-step/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.9116     | 8.9116     | 8.9116     |   0.0 | 39.40
+Neigh   | 0.26535    | 0.26535    | 0.26535    |   0.0 |  1.17
+Comm    | 0.65637    | 0.65637    | 0.65637    |   0.0 |  2.90
+Output  | 0.0036141  | 0.0036141  | 0.0036141  |   0.0 |  0.02
+Modify  | 12.725     | 12.725     | 12.725     |   0.0 | 56.26
+Other   |            | 0.05425    |            |       |  0.24
+
+Nlocal:             54 ave          54 max          54 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            632 ave         632 max         632 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1677 ave        1677 max        1677 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:         3354 ave        3354 max        3354 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3354
+Ave neighs/atom = 62.111111
+Neighbor list builds = 1000
+Dangerous builds = 1000
+Total wall time: 0:00:22

examples/SPIN/test_problems/validation_nvt/log.11Mar25.spin.nvt_spin.g++.1

@@ -0,0 +1,241 @@
+LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-169-g4246fab500)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+# bcc iron in a 3d periodic box
+
+clear
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
+  using 1 OpenMP thread(s) per MPI task
+units 		metal
+atom_style 	spin
+# atom_style 	spin/kk
+
+dimension 	3
+boundary 	p p p
+
+# necessary for the serial algorithm (sametag)
+atom_modify 	map array
+
+lattice 	bcc 2.8665
+Lattice spacing in x,y,z = 2.8665 2.8665 2.8665
+region 		box block 0.0 3.0 0.0 3.0 0.0 3.0
+create_box 	1 box
+Created orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
+  1 by 1 by 1 MPI processor grid
+create_atoms 	1 box
+Created 54 atoms
+  using lattice units in orthogonal box = (0 0 0) to (8.5995 8.5995 8.5995)
+  create_atoms CPU = 0.001 seconds
+
+# setting mass, mag. moments, and interactions for bcc iron
+
+mass		1 55.845
+set 		group all spin 2.2 0.0 0.0 1.0
+Setting atom values ...
+WARNING: Set attribute spin is deprecated. Please use spin/atom instead. (src/set.cpp:268)
+  54 settings made for spin
+velocity 	all create 0 4928459 rot yes dist gaussian
+
+# pair_style 	hybrid/overlay eam/alloy spin/exchange 3.5
+pair_style 	hybrid/overlay eam/alloy spin/exchange 4.0 spin/neel 4.0
+pair_coeff 	* * eam/alloy Fe_Mishin2006.eam.alloy Fe
+pair_coeff 	* * spin/exchange exchange 3.4 0.1 0.2171 1.841
+pair_coeff 	* * spin/neel neel 4.0 0.02 0.0 1.841 0.0 0.0 1.0
+
+neighbor 	0.1 bin
+neigh_modify 	every 10 check yes delay 20
+
+fix 		1 all precession/spin zeeman 0.0 0.0 0.0 1.0
+fix         2 all langevin 0.0 0.0 0.001 48279
+fix 		3 all langevin/spin 200.0 0.01 321
+fix 		4 all nve/spin lattice moving
+timestep	0.001
+
+# compute and output options
+
+compute 	out_mag    all spin
+compute 	out_pe     all pe
+compute 	out_ke     all ke
+compute 	out_temp   all temp
+
+variable 	emag      equal c_out_mag[5]
+variable 	tmag      equal c_out_mag[6]
+
+thermo_style    custom step time v_tmag temp v_emag ke pe etotal
+thermo          200
+
+run 		20000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- fix nve/spin command: doi:10.1016/j.jcp.2018.06.042
+
+@article{tranchida2018massively,
+title={Massively Parallel Symplectic Algorithm for Coupled Magnetic Spin    Dynamics and Molecular Dynamics},
+author={Tranchida, J and Plimpton, S J and Thibaudeau, P and Thompson, A P},
+journal={Journal of Computational Physics},
+volume={372},
+pages={406--425},
+year={2018},
+publisher={Elsevier}
+doi={10.1016/j.jcp.2018.06.042}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Neighbor list info ...
+  update: every = 10 steps, delay = 20 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.773367
+  ghost atom cutoff = 5.773367
+  binsize = 2.8866835, bins = 3 3 3
+  3 neighbor lists, perpetual/occasional/extra = 3 0 0
+  (1) pair eam/alloy, perpetual, half/full from (2)
+      attributes: half, newton on, cut 5.7733670002446
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair spin/exchange, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+  (3) pair spin/neel, perpetual, copy from (2)
+      attributes: full, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 6.008 | 6.008 | 6.008 Mbytes
+   Step          Time          v_tmag          Temp          v_emag         KinEng         PotEng         TotEng    
+         0   0              1.4336203e-31  0             -22.021022      0             -253.14103     -253.14103    
+       200   0.2            185.03537      7.1508965e-05 -21.172867      4.8989274e-07 -252.29287     -252.29287    
+       400   0.4            209.70221      8.8414079e-05 -21.060203      6.0570608e-07 -252.1802      -252.1802     
+       600   0.6            185.48899      0.00010245242 -21.112413      7.0187977e-07 -252.23241     -252.23241    
+       800   0.8            223.05275      8.1457051e-05 -21.018423      5.5804496e-07 -252.13842     -252.13842    
+      1000   1              213.0164       8.9515898e-05 -21.048926      6.1325441e-07 -252.16892     -252.16892    
+      1200   1.2            246.36673      0.0001154676  -20.930718      7.9104402e-07 -252.05072     -252.05072    
+      1400   1.4            196.53774      6.2911172e-05 -21.154732      4.3099109e-07 -252.27473     -252.27473    
+      1600   1.6            182.01716      0.00010355261 -21.16282       7.0941692e-07 -252.28282     -252.28282    
+      1800   1.8            210.96677      8.7541641e-05 -21.088701      5.997292e-07  -252.2087      -252.2087     
+      2000   2              253.99717      0.00010826381 -20.86351       7.416924e-07  -251.98351     -251.98351    
+      2200   2.2            216.1501       9.6113637e-05 -21.030784      6.5845412e-07 -252.15078     -252.15078    
+      2400   2.4            223.43699      8.5950374e-05 -21.009537      5.8882776e-07 -252.12954     -252.12954    
+      2600   2.6            218.14727      0.00010110952 -20.970036      6.9267987e-07 -252.09004     -252.09004    
+      2800   2.8            232.40923      0.00011013217 -20.973661      7.5449212e-07 -252.09366     -252.09366    
+      3000   3              237.03942      0.0001227047  -20.923005      8.4062388e-07 -252.043       -252.043      
+      3200   3.2            193.18057      6.4453691e-05 -21.192632      4.4155855e-07 -252.31263     -252.31263    
+      3400   3.4            215.89559      0.00010926778 -20.99777       7.4857038e-07 -252.11777     -252.11777    
+      3600   3.6            166.54235      7.286928e-05  -21.241556      4.9921196e-07 -252.36156     -252.36156    
+      3800   3.8            159.38579      5.7560855e-05 -21.290065      3.9433719e-07 -252.41007     -252.41007    
+      4000   4              170.59358      7.7217892e-05 -21.234059      5.2900339e-07 -252.35406     -252.35406    
+      4200   4.2            215.77287      8.7497504e-05 -21.031438      5.9942683e-07 -252.15144     -252.15144    
+      4400   4.4            197.99439      8.3188835e-05 -21.136708      5.6990905e-07 -252.25671     -252.25671    
+      4600   4.6            225.89271      0.00015400081 -20.963516      1.0550269e-06 -252.08352     -252.08352    
+      4800   4.8            202.99311      0.00014034452 -21.013112      9.614705e-07  -252.13311     -252.13311    
+      5000   5              213.82643      0.00011505981 -21.058401      7.8825036e-07 -252.1784      -252.1784     
+      5200   5.2            185.50349      8.6160092e-05 -21.172207      5.902645e-07  -252.29221     -252.29221    
+      5400   5.4            201.98179      0.00010791717 -21.096481      7.3931764e-07 -252.21648     -252.21648    
+      5600   5.6            171.20549      6.8869235e-05 -21.197869      4.718085e-07  -252.31787     -252.31787    
+      5800   5.8            227.95465      0.00012603913 -21.009323      8.6346729e-07 -252.12932     -252.12932    
+      6000   6              200.21111      0.00010449734 -21.110701      7.1588912e-07 -252.2307      -252.2307     
+      6200   6.2            160.58077      7.2836942e-05 -21.267151      4.9899042e-07 -252.38715     -252.38715    
+      6400   6.4            200.05407      9.0509705e-05 -21.073988      6.2006277e-07 -252.19399     -252.19399    
+      6600   6.6            190.65275      0.0001033421  -21.158207      7.0797478e-07 -252.27821     -252.27821    
+      6800   6.8            228.26898      0.00014786596 -20.911618      1.0129983e-06 -252.03162     -252.03162    
+      7000   7              181.38559      7.164051e-05  -21.178965      4.9079392e-07 -252.29897     -252.29897    
+      7200   7.2            206.68689      0.00014900154 -20.996098      1.0207779e-06 -252.1161      -252.1161     
+      7400   7.4            192.31745      7.9639216e-05 -21.152927      5.4559136e-07 -252.27293     -252.27293    
+      7600   7.6            190.74433      8.1341909e-05 -21.140079      5.5725615e-07 -252.26008     -252.26008    
+      7800   7.8            174.0955       6.4367878e-05 -21.239195      4.4097067e-07 -252.3592      -252.35919    
+      8000   8              160.00011      0.00012761576 -21.159302      8.7426845e-07 -252.2793      -252.2793     
+      8200   8.2            210.43151      0.00014479042 -21.034928      9.9192846e-07 -252.15493     -252.15493    
+      8400   8.4            234.76455      0.00017824488 -20.929712      1.2211178e-06 -252.04971     -252.04971    
+      8600   8.6            186.41675      8.9522862e-05 -21.152624      6.1330212e-07 -252.27262     -252.27262    
+      8800   8.8            182.51437      8.1196096e-05 -21.169538      5.5625721e-07 -252.28954     -252.28954    
+      9000   9              205.7602       8.1712224e-05 -21.069704      5.597931e-07  -252.1897      -252.1897     
+      9200   9.2            169.12461      4.5311332e-05 -21.260803      3.1041832e-07 -252.3808      -252.3808     
+      9400   9.4            226.30809      0.00011391282 -20.976322      7.8039252e-07 -252.09632     -252.09632    
+      9600   9.6            167.17205      9.1023114e-05 -21.226931      6.2358003e-07 -252.34693     -252.34693    
+      9800   9.8            204.63476      0.00010727562 -21.045363      7.3492253e-07 -252.16536     -252.16536    
+     10000   10             236.18563      8.998006e-05  -20.973452      6.1643429e-07 -252.09345     -252.09345    
+     10200   10.2           194.32863      7.2352023e-05 -21.144235      4.9566835e-07 -252.26424     -252.26424    
+     10400   10.4           212.89479      0.00011913313 -21.041706      8.1615576e-07 -252.16171     -252.1617     
+     10600   10.6           215.20168      9.7714692e-05 -21.032571      6.6942261e-07 -252.15257     -252.15257    
+     10800   10.8           297.63322      0.00013498385 -20.721355      9.2474566e-07 -251.84135     -251.84135    
+     11000   11             221.40055      0.00010205784 -21.051231      6.9917662e-07 -252.17123     -252.17123    
+     11200   11.2           242.39307      0.00013617253 -20.890742      9.3288909e-07 -252.01074     -252.01074    
+     11400   11.4           165.26613      7.2237463e-05 -21.24741       4.9488352e-07 -252.36741     -252.36741    
+     11600   11.6           216.24435      8.1150764e-05 -21.036156      5.5594665e-07 -252.15616     -252.15616    
+     11800   11.8           183.53912      0.00010117662 -21.186918      6.9313953e-07 -252.30692     -252.30692    
+     12000   12             220.44994      9.647801e-05  -21.023611      6.6095036e-07 -252.14361     -252.14361    
+     12200   12.2           225.17986      9.472867e-05  -21.009823      6.48966e-07   -252.12982     -252.12982    
+     12400   12.4           216.68616      8.9352492e-05 -21.025818      6.1213495e-07 -252.14582     -252.14582    
+     12600   12.6           179.65027      6.5355297e-05 -21.199208      4.4773526e-07 -252.31921     -252.31921    
+     12800   12.8           210.22912      7.5167585e-05 -21.071447      5.1495716e-07 -252.19145     -252.19145    
+     13000   13             157.423        9.2895323e-05 -21.250615      6.3640614e-07 -252.37062     -252.37061    
+     13200   13.2           204.52025      0.00012645764 -21.049044      8.6633447e-07 -252.16904     -252.16904    
+     13400   13.4           198.28053      0.00012118522 -21.066084      8.3021421e-07 -252.18609     -252.18608    
+     13600   13.6           237.99318      8.644348e-05  -20.978488      5.9220593e-07 -252.09849     -252.09849    
+     13800   13.8           222.81023      0.00015789536 -20.951387      1.0817076e-06 -252.07139     -252.07139    
+     14000   14             218.31245      0.00011842157 -21.008674      8.1128101e-07 -252.12867     -252.12867    
+     14200   14.2           197.5018       0.00011399102 -21.081911      7.8092826e-07 -252.20191     -252.20191    
+     14400   14.4           228.11014      0.00015934606 -20.963235      1.091646e-06  -252.08323     -252.08323    
+     14600   14.6           216.45102      9.6033576e-05 -21.034352      6.5790564e-07 -252.15435     -252.15435    
+     14800   14.8           205.97376      0.00014278574 -21.018847      9.7819479e-07 -252.13885     -252.13885    
+     15000   15             230.09259      0.00012803086 -20.986446      8.7711221e-07 -252.10645     -252.10644    
+     15200   15.2           248.21379      0.0001784321  -20.84502       1.2224004e-06 -251.96502     -251.96502    
+     15400   15.4           223.07119      0.00013057001 -20.984451      8.9450744e-07 -252.10445     -252.10445    
+     15600   15.6           194.42126      8.4530618e-05 -21.127055      5.7910131e-07 -252.24705     -252.24705    
+     15800   15.8           207.23453      0.00013807606 -21.035173      9.4592974e-07 -252.15517     -252.15517    
+     16000   16             175.93234      8.2440767e-05 -21.208299      5.6478419e-07 -252.3283      -252.3283     
+     16200   16.2           225.63746      7.4767651e-05 -21.012845      5.1221731e-07 -252.13285     -252.13284    
+     16400   16.4           149.12667      6.624179e-05  -21.331981      4.5380844e-07 -252.45198     -252.45198    
+     16600   16.6           211.41275      0.00012606898 -21.042094      8.6367183e-07 -252.16209     -252.16209    
+     16800   16.8           199.88466      8.2345231e-05 -21.116203      5.641297e-07  -252.2362      -252.2362     
+     17000   17             212.37144      0.00010445794 -21.041826      7.1561919e-07 -252.16183     -252.16183    
+     17200   17.2           160.83603      5.4109632e-05 -21.294207      3.706936e-07  -252.41421     -252.41421    
+     17400   17.4           254.84209      0.00013687967 -20.886397      9.3773358e-07 -252.0064      -252.0064     
+     17600   17.6           237.6091       0.00012462019 -20.958967      8.5374644e-07 -252.07897     -252.07897    
+     17800   17.8           194.26242      7.0286952e-05 -21.145006      4.8152099e-07 -252.26501     -252.26501    
+     18000   18             175.14964      6.1470052e-05 -21.239458      4.2111827e-07 -252.35946     -252.35946    
+     18200   18.2           181.99258      7.2295849e-05 -21.195184      4.9528351e-07 -252.31519     -252.31519    
+     18400   18.4           197.11115      9.9207898e-05 -21.116471      6.7965225e-07 -252.23647     -252.23647    
+     18600   18.6           211.2814       8.4543325e-05 -21.074729      5.7918837e-07 -252.19473     -252.19473    
+     18800   18.8           198.62813      9.4052117e-05 -21.097909      6.4433109e-07 -252.21791     -252.21791    
+     19000   19             226.11003      0.00013827389 -20.951669      9.4728506e-07 -252.07167     -252.07167    
+     19200   19.2           233.61049      0.00013363448 -20.917911      9.1550145e-07 -252.03791     -252.03791    
+     19400   19.4           182.94749      9.0400181e-05 -21.139686      6.1931245e-07 -252.25969     -252.25968    
+     19600   19.6           155.99677      5.9871119e-05 -21.282519      4.1016433e-07 -252.40252     -252.40252    
+     19800   19.8           179.57217      8.5624245e-05 -21.193447      5.8659353e-07 -252.31345     -252.31345    
+     20000   20             243.60222      0.00015451915 -20.911769      1.0585779e-06 -252.03177     -252.03177    
+Loop time of 21.9748 on 1 procs for 20000 steps with 54 atoms
+
+Performance: 78.636 ns/day, 0.305 hours/ns, 910.134 timesteps/s, 49.147 katom-step/s
+100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.1863     | 8.1863     | 8.1863     |   0.0 | 37.25
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.77445    | 0.77445    | 0.77445    |   0.0 |  3.52
+Output  | 0.0037256  | 0.0037256  | 0.0037256  |   0.0 |  0.02
+Modify  | 12.954     | 12.954     | 12.954     |   0.0 | 58.95
+Other   |            | 0.05601    |            |       |  0.25
+
+Nlocal:             54 ave          54 max          54 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            801 ave         801 max         801 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:           1728 ave        1728 max        1728 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:         3456 ave        3456 max        3456 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 3456
+Ave neighs/atom = 64
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:22

examples/rerun/in.rdf.first

@@ -27,7 +27,7 @@ neigh_modify	delay 0 every 20 check no
 
 fix		1 all nve
 
-dump            1 all custom 100 lj.dump id type x y z
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
 
 compute         myRDF all rdf 50 cutoff 2.5
 fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector