lammps · akohlmey · Mar 11, 2022 · Mar 1, 2022 · Mar 2, 2022 · Mar 2, 2022
diff --git a/doc/src/Build_settings.rst b/doc/src/Build_settings.rst
@@ -4,15 +4,15 @@ Optional build settings
 LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
-* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
-* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
-* :ref:`Size of LAMMPS integer types <size>`
-* :ref:`Read or write compressed files <gzip>`
-* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
-* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
-* :ref:`Memory allocation alignment <align>`
-* :ref:`Workaround for long long integers <longlong>`
-* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library
+* `C++11 standard compliance`_ when building all of LAMMPS
+* `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
+* `Size of LAMMPS integer types and size limits`_
+* `Read or write compressed files`_
+* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
+* `Memory allocation alignment`_
+* `Workaround for long long integers`_
+* `Exception handling when using LAMMPS as a library`_ to capture errors
+* `Trigger selected floating-point exceptions`_
 
 ----------
 

diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst
@@ -142,11 +142,11 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
-   * :doc:`stress/cartesian <compute_stress_cartesian>`
-   * :doc:`stress/cylinder <compute_stress_cartesian>`
+   * :doc:`stress/cartesian <compute_stress_profile>`
+   * :doc:`stress/cylinder <compute_stress_profile>`
    * :doc:`stress/mop <compute_stress_mop>`
    * :doc:`stress/mop/profile <compute_stress_mop>`
-   * :doc:`stress/spherical <compute_stress_cartesian>`
+   * :doc:`stress/spherical <compute_stress_profile>`
    * :doc:`stress/tally <compute_tally>`
    * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
    * :doc:`temp (k) <compute_temp>`

diff --git a/doc/src/Developer_notes.rst b/doc/src/Developer_notes.rst
@@ -25,18 +25,17 @@ following benefits:
 - transparent support for translating unsupported UTF-8 characters to their ASCII equivalents
   (the text-to-value conversion functions **only** accept ASCII characters)
 
-In most cases (e.g. potential files) the same data is needed on all
-MPI ranks.  Then it is best to do the reading and parsing only on MPI
-rank 0, and communicate the data later with one or more
-``MPI_Bcast()`` calls.  For reading generic text and potential
-parameter files the custom classes :cpp:class:`TextFileReader
-<LAMMPS_NS::TextFileReader>` and :cpp:class:`PotentialFileReader
-<LAMMPS_NS::PotentialFileReader>` are available. They allow reading
-the file as individual lines for which they can return a tokenizer
-class (see below) for parsing the line.  Or they can return blocks of
-numbers as a vector directly.  The documentation on `File reader
-classes <file-reader-classes>`_ contains an example for a typical
-case.
+In most cases (e.g. potential files) the same data is needed on all MPI
+ranks.  Then it is best to do the reading and parsing only on MPI rank
+0, and communicate the data later with one or more ``MPI_Bcast()``
+calls.  For reading generic text and potential parameter files the
+custom classes :cpp:class:`TextFileReader <LAMMPS_NS::TextFileReader>`
+and :cpp:class:`PotentialFileReader <LAMMPS_NS::PotentialFileReader>`
+are available. They allow reading the file as individual lines for which
+they can return a tokenizer class (see below) for parsing the line.  Or
+they can return blocks of numbers as a vector directly.  The
+documentation on :ref:`File reader classes <file-reader-classes>`
+contains an example for a typical case.
 
 When reading per-atom data, the data on each line of the file usually
 needs to include an atom ID so it can be associated with a particular

diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst
@@ -252,12 +252,6 @@ follows:
 - The Timer class logs timing information, output at the end
   of a run.
 
-.. TODO section on "Spatial decomposition and parallel operations"
-..       diagram of 3d processor grid, brick vs. tiled. local vs. ghost
-..       atoms, 6-way communication with pack/unpack functions,
-..       PBC as part of the communication, forward and reverse communication
-..       rendezvous communication, ring communication.
-
 .. TODO section on "Fixes, Computes, and Variables"
 ..      how and when data is computed and provided and how it is
 ..      referenced. flags in Fix/Compute/Variable classes tell

diff --git a/doc/src/Developer_utils.rst b/doc/src/Developer_utils.rst
@@ -396,7 +396,7 @@ A typical code segment would look like this:
 
 ----------
 
-.. file-reader-classes:
+.. _file-reader-classes:
 
 File reader classes
 -------------------

diff --git a/doc/src/compute.rst b/doc/src/compute.rst
@@ -288,11 +288,11 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`sph/t/atom <compute_sph_t_atom>` - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
 * :doc:`spin <compute_spin>` - magnetic quantities for a system of atoms having spins
 * :doc:`stress/atom <compute_stress_atom>` - stress tensor for each atom
-* :doc:`stress/cartesian <compute_stress_cartesian>` - stress tensor in cartesian coordinates
-* :doc:`stress/cylinder <compute_stress_cartesian>` - stress tensor in cylindrical coordinates
+* :doc:`stress/cartesian <compute_stress_profile>` - stress tensor in cartesian coordinates
+* :doc:`stress/cylinder <compute_stress_profile>` - stress tensor in cylindrical coordinates
 * :doc:`stress/mop <compute_stress_mop>` - normal components of the local stress tensor using the method of planes
 * :doc:`stress/mop/profile <compute_stress_mop>` - profile of the normal components of the local stress tensor using the method of planes
-* :doc:`stress/spherical <compute_stress_cartesian>` - stress tensor in spherical coordinates
+* :doc:`stress/spherical <compute_stress_profile>` - stress tensor in spherical coordinates
 * :doc:`stress/tally <compute_tally>` - stress between two groups of atoms via the tally callback mechanism
 * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>` - per-atom chemical concentration of a specified species for each tDPD particle
 * :doc:`temp <compute_temp>` - temperature of group of atoms

diff --git a/doc/src/compute_momentum.rst b/doc/src/compute_momentum.rst
@@ -23,11 +23,10 @@ Examples
 Description
 """""""""""
 
-Define a computation that calculates the translational momentum
-of a group of particles.
-
-The momentum of each particles is computed as m v, where m and v are
-the mass and velocity of the particle.
+Define a computation that calculates the translational momentum *p*
+of a group of particles.  It is computed as the sum :math:`\vec{p} = \sum_i m_i \cdot \vec{v}_i`
+over all particles in the compute group, where *m* and *v* are
+the mass and velocity vector of the particle, respectively.
 
 Output info
 """""""""""

diff --git a/doc/src/compute_stress_mop.rst b/doc/src/compute_stress_mop.rst
@@ -73,7 +73,7 @@ command, since those are contributions to the global system pressure.
 
 NOTE 3: The local stress profile generated by compute *stress/mop/profile*
 is similar to that obtained by compute
-:doc:`stress/cartesian <compute_stress_cartesian>`.
+:doc:`stress/cartesian <compute_stress_profile>`.
 A key difference
 is that compute *stress/mop/profile* considers particles
 crossing a set of planes,
@@ -122,7 +122,7 @@ intra-molecular interactions, and long range (kspace) interactions.
 Related commands
 """"""""""""""""
 
-:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_cartesian>`, :doc:`compute stress/cylinder <compute_stress_cartesian>`, :doc:`compute stress/spherical <compute_stress_cartesian>`
+:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
 
 Default
 """""""

diff --git a/doc/src/compute_stress_cartesian.rst → doc/src/compute_stress_profile.rst b/doc/src/compute_stress_cartesian.rst → doc/src/compute_stress_profile.rst
diff --git a/doc/src/compute_tally.rst b/doc/src/compute_tally.rst
@@ -31,7 +31,7 @@ Syntax
    compute ID group-ID style group2-ID
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
-* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or * or *pe/tally* or *pe/mol/tally* or *stress/tally*
+* style = *force/tally* or *heat/flux/tally* or *heat/flux/virial/tally* or *pe/tally* or *pe/mol/tally* or *stress/tally*
 * group2-ID = group ID of second (or same) group
 
 Examples
@@ -61,7 +61,7 @@ mechanism. Compute *pe/mol/tally* is one such style, that can
 - through using this mechanism - separately tally intermolecular
 and intramolecular energies. Something that would otherwise be
 impossible without integrating this as a core functionality into
-the based classes of LAMMPS.
+the base classes of LAMMPS.
 
 ----------
 
@@ -148,30 +148,38 @@ pairwise property computations.
 Output info
 """""""""""
 
-Compute *pe/tally* calculates a global scalar (the energy) and a per
-atom scalar (the contributions of the single atom to the global
-scalar). Compute *pe/mol/tally* calculates a global 4-element vector
-containing (in this order): *evdwl* and *ecoul* for intramolecular pairs
-and *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
-identified by their molecule IDs, the partitioning does not have to be
-related to molecules, but the energies are tallied into the respective
-slots depending on whether the molecule IDs of a pair are the same or
-different. Compute *force/tally* calculates a global scalar (the force
-magnitude) and a per atom 3-element vector (force contribution from
-each atom).  Compute *stress/tally* calculates a global scalar
-(average of the diagonal elements of the stress tensor) and a per atom
-vector (the 6 elements of stress tensor contributions from the
-individual atom). As in :doc:`compute heat/flux <compute_heat_flux>`,
-compute *heat/flux/tally* calculates a global vector of length 6,
-where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
-components of the full heat flow vector,
-and the next 3 components are the corresponding components
-of just the convective portion of the flow, i.e. the
-first term in the equation for :math:`\mathbf{Q}`.
-Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
-and a per atom 3-element vector
-(contribution to the force acting over atoms in the first group
-from individual atoms in both groups).
+- Compute *pe/tally* calculates a global scalar (the energy) and a per
+  atom scalar (the contributions of the single atom to the global
+  scalar).
+
+- Compute *pe/mol/tally* calculates a global 4-element vector containing
+  (in this order): *evdwl* and *ecoul* for intramolecular pairs and
+  *evdwl* and *ecoul* for intermolecular pairs. Since molecules are
+  identified by their molecule IDs, the partitioning does not have to be
+  related to molecules, but the energies are tallied into the respective
+  slots depending on whether the molecule IDs of a pair are the same or
+  different.
+
+- Compute *force/tally* calculates a global scalar (the force magnitude)
+  and a per atom 3-element vector (force contribution from each atom).
+
+- Compute *stress/tally* calculates a global scalar
+  (average of the diagonal elements of the stress tensor) and a per atom
+  vector (the 6 elements of stress tensor contributions from the
+  individual atom).
+
+- As in :doc:`compute heat/flux <compute_heat_flux>`,
+  compute *heat/flux/tally* calculates a global vector of length 6,
+  where the first 3 components are the :math:`x`, :math:`y`, :math:`z`
+  components of the full heat flow vector,
+  and the next 3 components are the corresponding components
+  of just the convective portion of the flow, i.e. the
+  first term in the equation for :math:`\mathbf{Q}`.
+
+- Compute *heat/flux/virial/tally* calculates a global scalar (heat flow)
+  and a per atom 3-element vector
+  (contribution to the force acting over atoms in the first group
+  from individual atoms in both groups).
 
 Both the scalar and vector values calculated by this compute are
 "extensive".

diff --git a/src/.gitignore b/src/.gitignore
@@ -1,6 +1,7 @@
 /Makefile.package
 /Makefile.package.settings
 /MAKE/MINE
+/ADIOS/Makefile.lammps
 /Make.py.last
 /lmp_*
 
@@ -267,6 +268,8 @@
 /fix_drag.h
 /fix_numdiff.cpp
 /fix_numdiff.h
+/fix_numdiff_virial.cpp
+/fix_numdiff_virial.h
 /fix_spring_rg.cpp
 /fix_spring_rg.h
 /fix_temp_csld.cpp
@@ -934,6 +937,8 @@
 /msm_cg.h
 /neb.cpp
 /neb.h
+/netcdf_units.cpp
+/netcdf_units.h
 /pair_adp.cpp
 /pair_adp.h
 /pair_agni.cpp
@@ -1069,6 +1074,8 @@
 /pair_hdnnp.h
 /pair_ilp_graphene_hbn.cpp
 /pair_ilp_graphene_hbn.h
+/pair_ilp_tmd.cpp
+/pair_ilp_tmd.h
 /pair_kolmogorov_crespi_full.cpp
 /pair_kolmogorov_crespi_full.h
 /pair_kolmogorov_crespi_z.cpp
@@ -1175,8 +1182,8 @@
 /pair_nm_cut_coul_cut.h
 /pair_nm_cut_coul_long.cpp
 /pair_nm_cut_coul_long.h
-/pait_nm_cut_split.cpp
-/pait_nm_cut_split.h
+/pair_nm_cut_split.cpp
+/pair_nm_cut_split.h
 /pair_oxdna_*.cpp
 /pair_oxdna_*.h
 /pair_oxdna2_*.cpp
@@ -1202,6 +1209,8 @@
 /pair_rebo.h
 /pair_resquared.cpp
 /pair_resquared.h
+/pair_saip_metal.cpp
+/pair_saip_metal.h
 /pair_sdpd_taitwater_isothermal.cpp
 /pair_sdpd_taitwater_isothermal.h
 /pair_sph_heatconduction.cpp