Merge branch 'develop' into always-exceptions

doc/src/Commands_compute.rst

@@ -63,7 +63,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
-   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere (k) <compute_erotate_sphere>`
    * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
    * :doc:`event/displace <compute_event_displace>`
    * :doc:`fabric <compute_fabric>`

doc/src/Commands_fix.rst

@@ -260,7 +260,7 @@ OPT.
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
    * :doc:`wall/colloid <fix_wall>`
    * :doc:`wall/ees <fix_wall_ees>`
-   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`
    * :doc:`wall/lj1043 <fix_wall>`

doc/src/Howto.rst

@@ -23,7 +23,6 @@ General howto
    Howto_library
    Howto_couple
    Howto_mdi
-   Howto_bpm
    Howto_broken_bonds
 
 Settings howto
@@ -83,6 +82,7 @@ Packages howto
    Howto_spherical
    Howto_granular
    Howto_body
+   Howto_bpm
    Howto_polarizable
    Howto_coreshell
    Howto_drude

doc/src/Manual.rst

@@ -136,10 +136,21 @@ Indices and tables
    :class: note
 
    The HTML version of the manual makes use of advanced features present
-   in "modern" web browsers.  This can lead to incompatibilities with older
+   in "modern" web browsers.  This leads to incompatibilities with older
-   web browsers (released more than 4 years ago) and specific vendor browsers
+   web browsers and specific vendor browsers (e.g. Internet Explorer on Windows)
-   (e.g. Internet Explorer on Windows; Microsoft Edge works well though)
    where parts of the pages are not rendered as expected (e.g. the layout is
    broken or mathematical expressions not typeset).  In that case we
    recommend to install/use a different/newer web browser or use
    the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.
+
+   The following web browser versions have been verified to work as
+   expected on Linux, macOS, and Windows where available:
+
+   - Safari version 11.1 and later
+   - Firefox version 54 and later
+   - Chrome version 54 and later
+   - Opera version 41 and later
+   - Edge version 80 and later
+
+   Also Android version 7.1 and later and iOS version 11 and later have
+   been verified to render this website as expected.

doc/src/Modify_contribute.rst

@@ -38,8 +38,8 @@ Packages versus individual files
 The remainder of this chapter describes how to add new "style" files of
 various kinds to LAMMPS.  Packages are simply collections of one or more
 such new class files which are invoked as a new style within a LAMMPS
-input script.  In some cases also collections of supporting functions or
+input script.  In some cases collections of supporting functions or
-classes are included as separate files in a package, especially when
+classes are also included as separate files in a package, especially when
 they can be shared between multiple styles. If designed correctly, these
 additions typically do not require any changes to the core code of
 LAMMPS; they are simply add-on files that are compiled with the rest of
@@ -88,8 +88,8 @@ Once you have prepared everything, see the :doc:`LAMMPS GitHub Tutorial
 new files through a GitHub pull request yourself.  If you are unable or
 unwilling to submit via GitHub yourself, you may also submit patch files
 or full files to the LAMMPS developers and ask them to submit a pull
-request on GitHub on your behalf.  Then create a gzipped tar file of
+request on GitHub on your behalf.  If this is the case, create a gzipped
-all  changed or added files or a corresponding patch file using
+tar file of all new or changed files or a corresponding patch file using
 'diff -u' or 'diff -c' format and compress it with gzip.  Please only
 use gzip compression, as this works well and is available on all platforms.
 

doc/src/Modify_gran_sub_mod.rst

@@ -80,8 +80,8 @@ There are also several type-specific methods
      - Optional method to test when particles are in contact. By default, this is when particles overlap.
    * - ``GranSubModNormal->pulloff_distance()``
      - Optional method to return the distance at which particles stop interacting. By default, this is when particles no longer overlap.
-   * - ``GranSubModNormal->calculate_area()``
+   * - ``GranSubModNormal->calculate_radius()``
-     - Optional method to return the surface area of the contact. By default, this returns the geometric cross section.
+     - Optional method to return the radius of the contact. By default, this returns the radius of the geometric cross section.
    * - ``GranSubModNormal->set_fncrit()``
      - Optional method that defines the critical force to break the contact used by some tangential, rolling, and twisting sub-models. By default, this is the current total normal force including damping.
    * - ``GranSubModNormal->calculate_forces()``
@@ -105,9 +105,7 @@ set of files ``gran_sub_mod_custom.h``:
 
    #ifdef GranSubMod_CLASS
    // clang-format off
-   GranSubModStyle(hooke/piecewise,
+   GranSubModStyle(hooke/piecewise,GranSubModNormalHookePiecewise,NORMAL);
-            GranSubModNormalHookePiecewise,
-            NORMAL);
    // clang-format on
    #else
 
@@ -119,15 +117,14 @@ set of files ``gran_sub_mod_custom.h``:
 
    namespace LAMMPS_NS {
    namespace Granular_NS {
-
+     class GranSubModNormalHookePiecewise : public GranSubModNormal {
-   class GranSubModNormalHookePiecewise : public GranSubModNormal {
+      public:
-    public:
+       GranSubModNormalHookePiecewise(class GranularModel *, class LAMMPS *);
-     GranSubModNormalHookePiecewise(class GranularModel *, class LAMMPS *);
+       void coeffs_to_local() override;
-     void coeffs_to_local() override;
+       double calculate_forces() override;
-     double calculate_forces();
+      protected:
-    protected:
+       double k1, k2, delta_switch;
-     double k1, k2, delta_switch;
+     };
-   };
 
    }    // namespace Granular_NS
    }    // namespace LAMMPS_NS
@@ -147,7 +144,8 @@ and ``gran_sub_mod_custom.cpp``
    using namespace LAMMPS_NS;
    using namespace Granular_NS;
 
-   GranSubModNormalHookePiecewise::GranSubModNormalHookePiecewise(GranularModel *gm, LAMMPS *lmp) :  GranSubModNormal(gm, lmp)
+   GranSubModNormalHookePiecewise::GranSubModNormalHookePiecewise(GranularModel *gm, LAMMPS *lmp) :
+       GranSubModNormal(gm, lmp)
    {
      num_coeffs = 4;
    }

doc/src/Modify_style.rst

@@ -40,13 +40,14 @@ conditions. This is the GNU public license in version 2 (not 3 or later)
 for the publicly distributed versions, e.g. on the LAMMPS homepage or on
 GitHub.  On request we also make a version of LAMMPS available under
 LGPL 2.1 terms; this will usually be the latest available or a previous
-stable version with a few LGPL 2.1 incompatible files removed.
+stable version with a few LGPL 2.1 incompatible files removed. More details
+are found on the :doc:`LAMMPS open-source license page <Intro_opensource>`.
 
 Your new source files should have the LAMMPS copyright, GPL notice, and
 your name and email address at the top, like other user-contributed
 LAMMPS source files.
 
-Contributions may be under a different license for long as that
+Contributions may be under a different license as long as that
 license does not conflict with the aforementioned terms.  Contributions
 that use code with a conflicting license can be split into two parts:
 
@@ -58,7 +59,7 @@ that use code with a conflicting license can be split into two parts:
 Please note, that this split licensed mode may complicate including the
 contribution in binary packages.
 
-Using Pull Requests on GitHub (preferred)
+Using pull requests on GitHub (preferred)
 -----------------------------------------
 
 All contributions to LAMMPS are processed as pull requests on GitHub
@@ -71,7 +72,7 @@ depends on the amount of time required to prepare the pull request and
 free time available by the LAMMPS developer in question to spend on this
 task.
 
-Integration Testing (strict)
+Integration testing (strict)
 ----------------------------
 
 Contributed code, like all pull requests, must pass the automated
@@ -159,7 +160,7 @@ decks.
   similar is acceptable when used to avoid unwanted domain decomposition
   of empty volumes).
 
-- outside of the log files no generated output should be included
+- outside of the log files, no generated output should be included
 
 - custom thermo_style settings may not include output measuring CPU or other time
   as that makes comparing the thermo output between different runs more complicated.
@@ -169,7 +170,7 @@ decks.
 
 - the total file size of all the inputs and outputs should be small
 
-- where possible potential files from the "potentials" folder or data
+- where possible, potential files from the "potentials" folder or data
   file from other folders should be re-used through symbolic links
 
 Howto document (optional)
@@ -187,7 +188,7 @@ your documentation, README files and examples, and the easier you make
 it for people to get started, the more likely it is that users will try
 out your new feature.
 
-Programming Style Requirements (varied)
+Programming style requirements (varied)
 ---------------------------------------
 
 The LAMMPS developers aim to employ a consistent programming style and
@@ -231,7 +232,7 @@ list all non-conforming lines.  By adding the `-f` flag to the command
 line, they will modify the flagged files to try removing the detected
 issues.
 
-Indentation and Placement of Braces (strongly preferred)
+Indentation and placement of braces (strongly preferred)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 LAMMPS uses 2 characters per indentation level and lines should be
@@ -240,7 +241,7 @@ kept within 100 characters wide.
 For new files added to the "src" tree, a `clang-format
 <https://clang.llvm.org/docs/ClangFormat.html>`_ configuration file is
 provided under the name `.clang-format`.  This file is compatible with
-clang-format version 8 and later. With that file present files can be
+clang-format version 8 and later. With that file present, files can be
 reformatted according to the configuration with a command like:
 `clang-format -i new-file.cpp`.  Ideally, this is done while writing the
 code or before a pull request is submitted.  Blocks of code where the
@@ -302,7 +303,7 @@ The core of LAMMPS is written in C++11 in a style that can be mostly
 described as "C with classes".  Advanced C++ features like operator
 overloading or excessive use of templates are avoided with the intent to
 keep the code readable to programmers that have limited C++ programming
-experience.  C++ constructs are acceptable when they help improving the
+experience.  C++ constructs are acceptable when they help improve the
 readability and reliability of the code, e.g. when using the
 `std::string` class instead of manipulating pointers and calling the
 string functions of the C library.  In addition a collection of
@@ -313,7 +314,7 @@ portability are provided.
 
 Included Fortran code has to be compatible with the Fortran 2003
 standard.  Python code must be compatible with Python 3.5.  Large parts
-or LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
+of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
 compatible with Python 2.7.  Compatibility with Python 2.7 is
 desirable, but compatibility with Python 3.5 is **required**.
 
@@ -432,7 +433,7 @@ you are uncertain, please ask.
 - Please use clang-format only to reformat files that you have
   contributed.  For header files containing a ``SomeStyle(keyword,
   ClassName)`` macros it is required to have this macro embedded with a
-  pair of ``// clang-format off``, ``// clang-format on`` commends and
+  pair of ``// clang-format off``, ``// clang-format on`` comments and
   the line must be terminated with a semi-colon (;).  Example:
 
   .. code-block:: c++

doc/src/angle_dipole.rst

@@ -28,15 +28,15 @@ The *dipole* angle style is used to control the orientation of a dipolar
 atom within a molecule :ref:`(Orsi) <Orsi>`. Specifically, the *dipole* angle
 style restrains the orientation of a point dipole :math:`\mu_j` (embedded in atom
 :math:`j`) with respect to a reference (bond) vector
-:math:`\vec{r_{ij}} = \vec{r_i} - \vec{r_j}`, where :math:`i` is another atom of
+:math:`\vec{r}_{ij} = \vec{r}_i - \vec{r}_j`, where :math:`i` is another atom of
 the same molecule (typically, :math:`i` and :math:`j` are also covalently bonded).
 
-It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu_j}`
+It is convenient to define an angle gamma between the 'free' vector :math:`\vec{\mu}_j`
-and the reference (bond) vector :math:`\vec{r_{ij}}`:
+and the reference (bond) vector :math:`\vec{r}_{ij}`:
 
 .. math::
 
-   \cos\gamma = \frac{\vec{\mu_j}\cdot\vec{r_{ij}}}{\mu_j\,r_{ij}}
+   \cos\gamma = \frac{\vec{\mu}_j\cdot\vec{r}_{ij}}{\mu_j\,r_{ij}}
 
 The *dipole* angle style uses the potential:
 
@@ -53,23 +53,23 @@ potential using the 'chain rule' as in appendix C.3 of
 
 .. math::
 
-   \vec{T_j} = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r_{ij}} \times \vec{\mu_j}
+   \vec{T}_j = \frac{2K(\cos\gamma - \cos\gamma_0)}{\mu_j\,r_{ij}}\, \vec{r}_{ij} \times \vec{\mu}_j
 
 Example: if :math:`\gamma_0` is set to 0 degrees, the torque generated by
 the potential will tend to align the dipole along the reference
-direction defined by the (bond) vector :math:`\vec{r_{ij}}` (in other words, :math:`\vec{\mu_j}` is
+direction defined by the (bond) vector :math:`\vec{r}_{ij}` (in other words, :math:`\vec{\mu}_j` is
 restrained to point towards atom :math:`i`).
 
-The dipolar torque :math:`\vec{T_j}` must be counterbalanced in order to conserve
+The dipolar torque :math:`\vec{T}_j` must be counterbalanced in order to conserve
 the local angular momentum. This is achieved via an additional force
-couple generating a torque equivalent to the opposite of :math:`\vec{T_j}`:
+couple generating a torque equivalent to the opposite of :math:`\vec{T}_j`:
 
 .. math::
 
-   -\vec{T_j} & = \vec{r_{ij}} \times \vec{F_i} \\
+   -\vec{T}_j & = \vec{r}_{ij} \times \vec{F}_i \\
-   \vec{F_j}  & = -\vec{F_i}
+   \vec{F}_j  & = -\vec{F}_i
 
-where :math:`\vec{F_i}` and :math:`\vec{F_j}` are applied on atoms :math:`i`
+where :math:`\vec{F}_i` and :math:`\vec{F}_j` are applied on atoms :math:`i`
 and :math:`j`, respectively.
 
 The following coefficients must be defined for each angle type via the

doc/src/compute_erotate_sphere.rst

@@ -1,8 +1,12 @@
 .. index:: compute erotate/sphere
+.. index:: compute erotate/sphere/kk
 
 compute erotate/sphere command
 ==============================
 
+Accelerator Variants: *erotate/sphere/kk*
+
+
 Syntax
 """"""
 
@@ -36,6 +40,12 @@ is the particle's angular velocity.
    spheres, not disks, meaning their moment of inertia will be the same
    as in 3d.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Output info
 """""""""""
 

doc/src/compute_ptm_atom.rst

@@ -66,8 +66,8 @@ The deviation is calculated as:
 
    \text{RMSD}(\mathbf{u}, \mathbf{v})
     = \min_{s, \mathbf{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
-   {\left\lVert s[\vec{u_i} - \mathbf{\bar{u}}]
+   {\left\lVert s[\vec{u}_i - \mathbf{\bar{u}}]
-                 - \mathbf{Q} \cdot \vec{v_i} \right\rVert}^2}
+                 - \mathbf{Q} \cdot \vec{v}_i \right\rVert}^2}
 
 Here, :math:`\vec u` and :math:`\vec v` contain the coordinates of the local
 and ideal structures respectively, :math:`s` is a scale factor, and

doc/src/compute_saed.rst

@@ -246,8 +246,9 @@ All array values calculated by this compute are "intensive".
 Restrictions
 """"""""""""
 
-This compute is part of the DIFFRACTION package.  It is only
+This compute is part of the DIFFRACTION package.  It is only enabled if
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 The compute_saed command does not work for triclinic cells.
 

doc/src/fix_dpd_source.rst

@@ -18,18 +18,21 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * edpd/source or tdpd/source = style name of this fix command
 * index (only specified for tdpd/source) = index of chemical species (1 to Nspecies)
-* keyword = *sphere* or *cuboid*
+* keyword = *sphere* or *cuboid* or *region*
 
   .. parsed-literal::
 
-       *sphere* values = cx,cy,cz,radius,source
+       *sphere* args = cx cy cz radius source
          cx,cy,cz = x,y,z center of spherical domain (distance units)
          radius = radius of a spherical domain (distance units)
          source = heat source or concentration source (flux units, see below)
-       *cuboid* values = cx,cy,cz,dLx,dLy,dLz,source
+       *cuboid* values = cx cy cz dLx dLy dLz source
-         cx,cy,cz = x,y,z lower left corner of a cuboid domain (distance units)
+         cx,cy,cz = x,y,z center of a cuboid domain (distance units)
          dLx,dLy,dLz = x,y,z side length of a cuboid domain (distance units)
          source = heat source or concentration source (flux units, see below)
+       *region* values = region-ID source
+         region = ID of region for heat or concentration source
+         source = heat source or concentration source (flux units, see below)
 
 Examples
 """"""""
@@ -40,6 +43,7 @@ Examples
    fix 1 all edpd/source cuboid 0.0 0.0 0.0 20.0 10.0 10.0 -0.01
    fix 1 all tdpd/source 1 sphere 5.0 0.0 0.0 5.0 0.01
    fix 1 all tdpd/source 2 cuboid 0.0 0.0 0.0 20.0 10.0 10.0 0.01
+   fix 1 all tdpd/source 1 region lower -0.01
 
 Description
 """""""""""
@@ -57,37 +61,50 @@ heat conduction with a source term (see Fig.12 in :ref:`(Li2014) <Li2014b>`)
 or diffusion with a source term (see Fig.1 in :ref:`(Li2015) <Li2015b>`), as
 an analog of a periodic Poiseuille flow problem.
 
-If the *sphere* keyword is used, the *cx,cy,cz,radius* defines a
+.. deprecated:: TBD
-spherical domain to apply the source flux to.
 
-If the *cuboid* keyword is used, the *cx,cy,cz,dLx,dLy,dLz* defines a
+   The *sphere* and *cuboid* keywords will be removed in a future version
-cuboid domain to apply the source flux to.
+   of LAMMPS.  The same functionality and more can be achieved with a region.
+
+If the *sphere* keyword is used, the *cx, cy, cz, radius* values define
+a spherical domain to apply the source flux to.
+
+If the *cuboid* keyword is used, the *cx, cy, cz, dLx, dLy, dLz* define
+a cuboid domain to apply the source flux to.
+
+If the *region* keyword is used, the *region-ID* selects which
+:doc:`region <region>` to apply the source flux to.
 
 ----------
 
 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 of these fixes 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 these fixes.  No global or per-atom quantities are stored by
-No parameter of this fix can be used with the *start/stop* keywords of
+these fixes for access by various :doc:`output commands <Howto_output>`.
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+No parameter of these fixes can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  These fixes are not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This fix is part of the DPD-MESO package. It is only enabled if
+These fixes are part of the DPD-MESO package.  They are only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
-Fix *edpd/source* must be used with the :doc:`pair_style edpd <pair_mesodpd>` command.  Fix *tdpd/source* must be used with the
+Fix *edpd/source* must be used with the :doc:`pair_style edpd
+<pair_mesodpd>` command.  Fix *tdpd/source* must be used with the
 :doc:`pair_style tdpd <pair_mesodpd>` command.
 
 Related commands
 """"""""""""""""
 
 :doc:`pair_style edpd <pair_mesodpd>`, :doc:`pair_style tdpd <pair_mesodpd>`,
-:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`, :doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
+:doc:`compute edpd/temp/atom <compute_edpd_temp_atom>`,
+:doc:`compute tdpd/cc/atom <compute_tdpd_cc_atom>`
 
 Default
 """""""

doc/src/fix_mdi_qm.rst

@@ -280,20 +280,25 @@ invoked by the :doc:`minimize <minimize>` command.
 Restrictions
 """"""""""""
 
-This command is part of the MDI package.  It is only enabled if
+This fix is part of the MDI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the :doc:`Build package
+was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
-codes (MD or QM codes), the :doc:`units <units>` command should be
+codes (MD or QM codes), the :doc:`units <units>` command should be used
-used to specify *real* or *metal* units.  This will ensure the correct
+to specify *real* or *metal* units.  This will ensure the correct unit
-unit conversions between LAMMPS and MDI units.  The other code will
+conversions between LAMMPS and MDI units.  The other code will also
-also perform similar unit conversions into its preferred units.
+perform similar unit conversions into its preferred units.
 
 LAMMPS can also be used as an MDI driver in other unit choices it
 supports, e.g. *lj*, but then no unit conversion to MDI units is
 performed.
 
+If this fix is used in conjunction with a QM code that does not support
+periodic boundary conditions (more specifically, a QM code that does not
+support the ``>CELL`` MDI command), the LAMMPS system must be fully
+non-periodic.  I.e. no dimension of the system can be periodic.
+
 Related commands
 """"""""""""""""
 

doc/src/fix_mdi_qmmm.rst

@@ -251,15 +251,20 @@ minimization, invoked by the :doc:`minimize <minimize>` command.
 Restrictions
 """"""""""""
 
-This command is part of the MDI package.  It is only enabled if
+This command is part of the MDI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the :doc:`Build package
+was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
 To use LAMMPS as an MDI driver in conjunction with other MDI-enabled
-codes (MD or QM codes), the :doc:`units <units>` command should be
+codes (MD or QM codes), the :doc:`units <units>` command should be used
-used to specify *real* or *metal* units.  This will ensure the correct
+to specify *real* or *metal* units.  This will ensure the correct unit
-unit conversions between LAMMPS and MDI units.  The other code will
+conversions between LAMMPS and MDI units.  The other code will also
-also perform similar unit conversions into its preferred units.
+perform similar unit conversions into its preferred units.
+
+If this fix is used in conjunction with a QM code that does not support
+periodic boundary conditions (more specifically, a QM code that does not
+support the ``>CELL`` MDI command), the LAMMPS system must be fully
+non-periodic.  I.e. no dimension of the system can be periodic.
 
 Related commands
 """"""""""""""""

doc/src/fix_precession_spin.rst

@@ -103,15 +103,15 @@ possible easy axis for the magnetic spins in the defined group:
 
    H_{cubic} = -\sum_{{ i}=1}^{N} K_{1}
    \Big[
-   \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n}_1 \right)^2
-   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2 +
+   \left(\vec{s}_{i} \cdot \vec{n}_2 \right)^2 +
-   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n}_2 \right)^2
-   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 +
+   \left(\vec{s}_{i} \cdot \vec{n}_3 \right)^2 +
-   \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n}_1 \right)^2
-   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2 \Big]
+   \left(\vec{s}_{i} \cdot \vec{n}_3 \right)^2 \Big]
-   +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n_1} \right)^2
+   +K_{2}^{(c)} \left(\vec{s}_{i} \cdot \vec{n}_1 \right)^2
-   \left(\vec{s}_{i} \cdot \vec{n_2} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n}_2 \right)^2
-   \left(\vec{s}_{i} \cdot \vec{n_3} \right)^2
+   \left(\vec{s}_{i} \cdot \vec{n}_3 \right)^2
 
 with :math:`K_1` and :math:`K_{2c}` (in eV) the intensity coefficients
 and :math:`\vec{n}_1`, :math:`\vec{n}_2` and :math:`\vec{n}_3`

doc/src/fix_saed_vtk.rst

@@ -163,11 +163,17 @@ intensity outputs.
 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
+This fix is part of the DIFFRACTION package.  It is only enabled if
-are relevant to this fix.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.
 
 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_wall_gran.rst

@@ -1,8 +1,11 @@
 .. index:: fix wall/gran
+.. index:: fix wall/gran/kk
 
 fix wall/gran command
 =====================
 
+Accelerator Variants: *wall/gran/kk*
+
 Syntax
 """"""
 
@@ -120,18 +123,17 @@ material.
 .. note::
 
    As discussed on the page for :doc:`pair_style gran/\* <pair_gran>`,
-   versions of LAMMPS before 9Jan09 used a
+   versions of LAMMPS before 9Jan09 used a different equation for
-   different equation for Hertzian interactions.  This means Hertizian
+   Hertzian interactions.  This means Hertizian wall/particle
-   wall/particle interactions have also changed.  They now include a
+   interactions have also changed.  They now include a sqrt(radius) term
-   sqrt(radius) term which was not present before.  Also the previous
+   which was not present before.  Also the previous versions used Kn and
-   versions used Kn and Kt from the pairwise interaction and hardwired
+   Kt from the pairwise interaction and hardwired dampflag to 1, rather
-   dampflag to 1, rather than letting them be specified directly.  This
+   than letting them be specified directly.  This means you can set the
-   means you can set the values of the wall/particle coefficients
+   values of the wall/particle coefficients appropriately in the current
-   appropriately in the current code to reproduce the results of a
+   code to reproduce the results of a previous Hertzian monodisperse
-   previous Hertzian monodisperse calculation.  For example, for the
+   calculation.  For example, for the common case of a monodisperse
-   common case of a monodisperse system with particles of diameter 1, Kn,
+   system with particles of diameter 1, Kn, Kt, gamma_n, and gamma_s
-   Kt, gamma_n, and gamma_s should be set sqrt(2.0) larger than they were
+   should be set sqrt(2.0) larger than they were previously.
-   previously.
 
 The effective mass *m_eff* in the formulas listed on the :doc:`pair_style granular <pair_gran>` page is the mass of the particle for
 particle/wall interactions (mass of wall is infinite).  If the
@@ -190,6 +192,12 @@ conduction model defined in :doc:`pair_style granular <pair_granular>`,
 heat flow, and :doc:`fix heat/flow <fix_heat_flow>` to integrate heat
 flow.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_amoeba.rst

@@ -94,22 +94,22 @@ The formulas for the AMOEBA energy terms are:
 
 .. math::
 
-   U_{hal} = \epsilon_{ij} \left( \frac{1.07}{\rho_{ij} + 0.07} \right)^7 \left( \frac{1.12}{\rho_{ij}^7 + 0.12} - 2 \right)
+   U_{hal} = & \epsilon_{ij} \left( \frac{1.07}{\rho_{ij} + 0.07} \right)^7 \left( \frac{1.12}{\rho_{ij}^7 + 0.12} - 2 \right) \\
-   U_{multipole} = \vec{M_i}\bold{T_{ij}}\vec{M_j}
+   U_{multipole} = & \vec{M}_i\boldsymbol{T_{ij}}\vec{M}_j, \quad \mbox{with} \quad
-      \vec{M} = \left( q, \vec{\mu_{perm}}, \bold{\Theta} \right)
+      \vec{M} = \left(q, \vec{\mu}_{perm}, \boldsymbol{\Theta} \right) \\
-   U_{polar} = \frac{1}{2}\vec{\mu_i}^{ind} \vec{E_i}^{perm}
+   U_{polar} = & \frac{1}{2}\vec{\mu}_i^{ind} \vec{E}_i^{perm}
 
 The formulas for the HIPPO energy terms are:
 
 .. math::
 
-   U_{multipole} = Z_i \frac{1}{r_{ij}} Z_j + Z_i T_{ij}^{damp} \vec{M_j} + Z_j T_{ji}^{damp} \vec{M_i} + \vec{M_i} T_{ij}^{damp} \vec{M_j}
+   U_{multipole} = & Z_i \frac{1}{r_{ij}} Z_j + Z_i T_{ij}^{damp} \vec{M}_j + Z_j T_{ji}^{damp} \vec{M}_i + \vec{M}_i T_{ij}^{damp} \vec{M}_j, \quad \mbox{with} \quad
-      \vec{M} = \left( Q, \vec{\mu_{perm}}, \bold{\Theta} \right)
+      \vec{M} = \left(q, \vec{\mu}_{perm}, \boldsymbol{\Theta} \right) \\
-   U_{polar} = \frac{1}{2}\vec{\mu_i}^{ind} \vec{E_i}^{perm}
+   U_{polar} = & \frac{1}{2}\vec{\mu}_i^{ind} \vec{E}_i^{perm} \\
-   U_{qxfer} = \epsilon_i e^{-\eta_j r_{ij}} + \epsilon_j e^{-\eta_i r_{ij}}
+   U_{qxfer} = & \epsilon_i e^{-\eta_j r_{ij}} + \epsilon_j e^{-\eta_i r_{ij}} \\
-   U_{repulsion} = \frac{K_i K_j}{r_{ij}} S^2
+   U_{repulsion} = & \frac{K_i K_j}{r_{ij}} S^2
-      S^2 = \left( \int{\phi_i \phi_j} dv \right)^2 = \vec{M_i}\bold{T_{ij}^{repulsion}}\vec{M_j}
+      S^2 = \left( \int{\phi_i \phi_j} dv \right)^2 = \vec{M}_i\boldsymbol{T_{ij}^{repulsion}}\vec{M}_j \\
-   U_{dispersion} = -\frac{C_6^iC_6^j}{r_{ij}^6} \left( f_{damp}^{dispersion} \right)_{ij}^2
+   U_{dispersion} = & -\frac{C_6^iC_6^j}{r_{ij}^6} \left( f_{damp}^{dispersion} \right)_{ij}^2
 
 .. note::
 

doc/src/pair_dipole.rst

@@ -96,29 +96,29 @@ force (F), and torque (T) between particles I and J.
                         \left(\frac{\sigma}{r}\right)^6 \right] \\
    E_{qq}  = & \frac{q_i q_j}{r} \\
    E_{qp}  = & \frac{q}{r^3} (p \bullet \vec{r}) \\
-   E_{pp}  = & \frac{1}{r^3} (\vec{p_i} \bullet \vec{p_j}) -
+   E_{pp}  = & \frac{1}{r^3} (\vec{p}_i \bullet \vec{p}_j) -
-             \frac{3}{r^5} (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r}) \\
+             \frac{3}{r^5} (\vec{p}_i \bullet \vec{r}) (\vec{p}_j \bullet \vec{r}) \\
              & \\
    F_{qq}  = & \frac{q_i q_j}{r^3} \vec{r} \\
    F_{qp}  = & -\frac{q}{r^3} \vec{p} + \frac{3q}{r^5}
              (\vec{p} \bullet \vec{r}) \vec{r} \\
-   F_{pp}  = & \frac{3}{r^5} (\vec{p_i} \bullet \vec{p_j}) \vec{r} -
+   F_{pp}  = & \frac{3}{r^5} (\vec{p}_i \bullet \vec{p}_j) \vec{r} -
-             \frac{15}{r^7} (\vec{p_i} \bullet \vec{r})
+             \frac{15}{r^7} (\vec{p}_i \bullet \vec{r})
-             (\vec{p_j} \bullet \vec{r}) \vec{r} +
+             (\vec{p}_j \bullet \vec{r}) \vec{r} +
-             \frac{3}{r^5} \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} +
+             \frac{3}{r^5} \left[ (\vec{p}_j \bullet \vec{r}) \vec{p}_i +
-             (\vec{p_i} \bullet \vec{r}) \vec{p_j} \right] \\
+             (\vec{p}_i \bullet \vec{r}) \vec{p}_j \right] \\
              & \\
-   T_{pq} = T_{ij}  = & \frac{q_j}{r^3} (\vec{p_i} \times \vec{r}) \\
+   T_{pq} = T_{ij}  = & \frac{q_j}{r^3} (\vec{p}_i \times \vec{r}) \\
-   T_{qp} = T_{ji}  = & - \frac{q_i}{r^3} (\vec{p_j} \times \vec{r}) \\
+   T_{qp} = T_{ji}  = & - \frac{q_i}{r^3} (\vec{p}_j \times \vec{r}) \\
-   T_{pp} = T_{ij}  = & -\frac{1}{r^3} (\vec{p_i} \times \vec{p_j}) +
+   T_{pp} = T_{ij}  = & -\frac{1}{r^3} (\vec{p}_i \times \vec{p}_j) +
-                      \frac{3}{r^5} (\vec{p_j} \bullet \vec{r})
+                      \frac{3}{r^5} (\vec{p}_j \bullet \vec{r})
-                      (\vec{p_i} \times \vec{r}) \\
+                      (\vec{p}_i \times \vec{r}) \\
-   T_{pp} = T_{ji}  = & -\frac{1}{r^3} (\vec{p_j} \times \vec{p_i}) +
+   T_{pp} = T_{ji}  = & -\frac{1}{r^3} (\vec{p}_j \times \vec{p}_i) +
-                      \frac{3}{r^5} (\vec{p_i} \bullet \vec{r})
+                      \frac{3}{r^5} (\vec{p}_i \bullet \vec{r})
-                      (\vec{p_j} \times \vec{r})
+                      (\vec{p}_j \times \vec{r})
 
 where :math:`q_i` and :math:`q_j` are the charges on the two
-particles, :math:`\vec{p_i}` and :math:`\vec{p_j}` are the dipole
+particles, :math:`\vec{p}_i` and :math:`\vec{p}_j` are the dipole
 moment vectors of the two particles, r is their separation distance,
 and the vector r = Ri - Rj is the separation vector between the two
 particles.  Note that Eqq and Fqq are simply Coulombic energy and
@@ -163,8 +163,8 @@ energy (E), force (F), and torque (T) between particles I and J:
   2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}\bullet\vec{r}) \\
   E_{pp} = & \left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
   3\left(\frac{r}{r_c}\right)^{\!4}\right]\left[\frac{1}{r^3}
-  (\vec{p_i} \bullet \vec{p_j}) - \frac{3}{r^5}
+  (\vec{p}_i \bullet \vec{p}_j) - \frac{3}{r^5}
-  (\vec{p_i} \bullet \vec{r}) (\vec{p_j} \bullet \vec{r})\right] \\
+  (\vec{p}_i \bullet \vec{r}) (\vec{p}_j \bullet \vec{r})\right] \\
            & \\
 
   F_{LJ}  = & \left\{\left[48\epsilon \left(\frac{\sigma}{r}\right)^{\!12} -
@@ -182,37 +182,37 @@ energy (E), force (F), and torque (T) between particles I and J:
   \frac{q}{r^3}\left[1-3\left(\frac{r}{r_c}\right)^{\!2} +
   2\left(\frac{r}{r_c}\right)^{\!3}\right] \vec{p} \\
   F_{pp}  = &\frac{3}{r^5}\Bigg\{\left[1-\left(\frac{r}{r_c}\right)^{\!4}\right]
-  \left[(\vec{p_i}\bullet\vec{p_j}) - \frac{3}{r^2} (\vec{p_i}\bullet\vec{r})
+  \left[(\vec{p}_i\bullet\vec{p}_j) - \frac{3}{r^2} (\vec{p}_i\bullet\vec{r})
-  (\vec{p_j} \bullet \vec{r})\right] \vec{r} + \\
+  (\vec{p}_j \bullet \vec{r})\right] \vec{r} + \\
     & \left[1 -
   4\left(\frac{r}{r_c}\right)^{\!3}+3\left(\frac{r}{r_c}\right)^{\!4}\right]
-  \left[ (\vec{p_j} \bullet \vec{r}) \vec{p_i} + (\vec{p_i} \bullet \vec{r})
+  \left[ (\vec{p}_j \bullet \vec{r}) \vec{p}_i + (\vec{p}_i \bullet \vec{r})
-  \vec{p_j} -\frac{2}{r^2} (\vec{p_i} \bullet \vec{r})
+  \vec{p}_j -\frac{2}{r^2} (\vec{p}_i \bullet \vec{r})
-  (\vec{p_j} \bullet \vec{r})\vec{r}\right] \Bigg\}
+  (\vec{p}_j \bullet \vec{r})\vec{r}\right] \Bigg\}
 
 .. math::
 
    T_{pq} = T_{ij}  = & \frac{q_j}{r^3} \left[ 1 -
   3\left(\frac{r}{r_c}\right)^{\!2} +
-  2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p_i}\times\vec{r}) \\
+  2\left(\frac{r}{r_c}\right)^{\!3}\right] (\vec{p}_i\times\vec{r}) \\
   T_{qp} = T_{ji}  = & - \frac{q_i}{r^3} \left[ 1 -
   3\left(\frac{r}{r_c}\right)^{\!2} +
-  2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p_j}\times\vec{r}) \\
+  2\left(\frac{r}{r_c}\right)^{\!3} \right] (\vec{p}_j\times\vec{r}) \\
   T_{pp} = T_{ij}  = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
-  e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \times \vec{p_j}) + \\
+  e3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p}_i \times \vec{p}_j) + \\
                      & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
-  3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_j}\bullet\vec{r})
+  3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p}_j\bullet\vec{r})
-  (\vec{p_i} \times \vec{r}) \\
+  (\vec{p}_i \times \vec{r}) \\
   T_{pp} = T_{ji} = & -\frac{1}{r^3}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
-  3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p_j} \times \vec{p_i}) + \\
+  3\left(\frac{r}{r_c}\right)^{\!4}\right](\vec{p}_j \times \vec{p}_i) + \\
                      & \frac{3}{r^5}\left[1-4\left(\frac{r}{r_c}\right)^{\!3} +
-  3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p_i} \bullet \vec{r})
+  3\left(\frac{r}{r_c}\right)^{\!4}\right] (\vec{p}_i \bullet \vec{r})
-  (\vec{p_j} \times \vec{r})
+  (\vec{p}_j \times \vec{r})
 
 where :math:`\epsilon` and :math:`\sigma` are the standard LJ
 parameters, :math:`r_c` is the cutoff, :math:`q_i` and :math:`q_j` are
-the charges on the two particles, :math:`\vec{p_i}` and
+the charges on the two particles, :math:`\vec{p}_i` and
-:math:`\vec{p_j}` are the dipole moment vectors of the two particles,
+:math:`\vec{p}_j` are the dipole moment vectors of the two particles,
 r is their separation distance, and the vector r = Ri - Rj is the
 separation vector between the two particles.  Note that Eqq and Fqq
 are simply Coulombic energy and force, Fij = -Fji as symmetric forces,

doc/src/pair_dpd.rst

@@ -68,13 +68,13 @@ of 3 terms
 
    \vec{f}  = & (F^C + F^D + F^R) \hat{r_{ij}} \qquad \qquad r < r_c \\
    F^C      = & A w(r) \\
-   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v_{ij}}) \\
+   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \\
    F^R      = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\
    w(r)     = & 1 - \frac{r}{r_c}
 
 where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
 force, and :math:`F^R` is a random force.  :math:`\hat{r_{ij}}` is a
-unit vector in the direction :math:`r_i - r_j`, :math:`\vec{v_{ij}}` is
+unit vector in the direction :math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
 the vector difference in velocities of the two atoms :math:`\vec{v}_i -
 \vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
 and unit variance, *dt* is the timestep size, and :math:`w(r)` is a

doc/src/pair_dpd_fdt.rst

@@ -56,13 +56,13 @@ given as a sum of 3 terms
 
    \vec{f}  = & (F^C + F^D + F^R) \hat{r_{ij}} \qquad \qquad r < r_c \\
    F^C      = & A w(r) \\
-   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v_{ij}}) \\
+   F^D      = & - \gamma w^2(r) (\hat{r_{ij}} \bullet \vec{v}_{ij}) \\
    F^R      = & \sigma w(r) \alpha (\Delta t)^{-1/2} \\
    w(r)     = & 1 - \frac{r}{r_c}
 
 where :math:`F^C` is a conservative force, :math:`F^D` is a dissipative
 force, and :math:`F^R` is a random force.  :math:`\hat{r_{ij}}` is a
-unit vector in the direction :math:`r_i - r_j`, :math:`\vec{v_{ij}}` is
+unit vector in the direction :math:`r_i - r_j`, :math:`\vec{v}_{ij}` is
 the vector difference in velocities of the two atoms, :math:`\vec{v}_i -
 \vec{v}_j`, :math:`\alpha` is a Gaussian random number with zero mean
 and unit variance, *dt* is the timestep size, and :math:`w(r)` is a
@@ -99,9 +99,9 @@ energies are computed within style *dpd/fdt/energy* as:
 .. math::
 
    du_{i}^{cond}  = & \kappa_{ij}(\frac{1}{\theta_{i}}-\frac{1}{\theta_{j}})\omega_{ij}^{2} + \alpha_{ij}\omega_{ij}\zeta_{ij}^{q}(\Delta{t})^{-1/2} \\
-   du_{i}^{mech}  = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})^{2} -
+   du_{i}^{mech}  = & -\frac{1}{2}\gamma_{ij}\omega_{ij}^{2}(\frac{\vec{r}_{ij}}{r_{ij}}\bullet\vec{v}_{ij})^{2} -
    \frac{\sigma^{2}_{ij}}{4}(\frac{1}{m_{i}}+\frac{1}{m_{j}})\omega_{ij}^{2} -
-   \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r_{ij}}}{r_{ij}}\bullet\vec{v_{ij}})\zeta_{ij}(\Delta{t})^{-1/2}
+   \frac{1}{2}\sigma_{ij}\omega_{ij}(\frac{\vec{r}_{ij}}{r_{ij}}\bullet\vec{v}_{ij})\zeta_{ij}(\Delta{t})^{-1/2}
 
 where
 

doc/src/pair_granular.rst

@@ -650,13 +650,13 @@ For *heat* *area*, the heat
 
 .. math::
 
-   Q = k_{s} a \Delta T
+   Q = k_{s} A \Delta T
 
 
 
 where :math:`\Delta T` is the difference in the two particles' temperature,
 :math:`k_{s}` is a non-negative numeric value for the conductivity, and
-:math:`a` is the area of the contact and depends on the normal force model.
+:math:`A` is the area of the contact and depends on the normal force model.
 
 Note that the option *none* must either be used in all or none of of the
 *pair_coeff* calls. See :doc:`fix heat/flow <fix_heat_flow>` and

doc/src/pair_pace.rst

@@ -48,9 +48,9 @@ Description
 
 Pair style *pace* computes interactions using the Atomic Cluster
 Expansion (ACE), which is a general expansion of the atomic energy in
-multi-body basis functions. :ref:`(Drautz) <Drautz20191>`.  The *pace*
+multi-body basis functions. :ref:`(Drautz19) <Drautz20191>`.  The *pace*
 pair style provides an efficient implementation that is described in
-this paper :ref:`(Lysogorskiy) <Lysogorskiy20211>`.
+this paper :ref:`(Lysogorskiy21) <Lysogorskiy20211>`.
 
 In ACE, the total energy is decomposed into a sum over atomic
 energies. The energy of atom *i* is expressed as a linear or non-linear
@@ -91,7 +91,7 @@ Extrapolation grade
 Calculation of extrapolation grade in PACE is implemented in `pair_style
 pace/extrapolation`.  It is based on the MaxVol algorithm similar to
 Moment Tensor Potential (MTP) by Shapeev et al.  and is described in
-:ref:`(Lysogorskiy2) <Lysogorskiy2022>`.  In order to compute
+:ref:`(Lysogorskiy23) <Lysogorskiy2023>`.  In order to compute
 extrapolation grade one needs to provide:
 
 #. ACE potential in B-basis form (`.yaml` format) and
@@ -182,12 +182,12 @@ recursive, chunksize = 4096,
 
 .. _Drautz20191:
 
-**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019).
+**(Drautz19)** Drautz, Phys Rev B, 99, 014104 (2019).
 
 .. _Lysogorskiy20211:
 
-**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+**(Lysogorskiy21)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
 
-.. _Lysogorskiy2022:
+.. _Lysogorskiy2023:
 
-**(Lysogorskiy2022)** Lysogorskiy, Bochkarev, Mrovec, Drautz, arXiv:2212.08716 (2022).
+**(Lysogorskiy23)** Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).

doc/src/pair_smtbq.rst

@@ -23,8 +23,9 @@ Description
 
 This pair style computes a variable charge SMTB-Q (Second-Moment
 tight-Binding QEq) potential as described in :ref:`SMTB-Q_1 <SMTB-Q_1>` and
-:ref:`SMTB-Q_2 <SMTB-Q_2>`. Briefly, the energy of metallic-oxygen systems
+:ref:`SMTB-Q_2 <SMTB-Q_2>`.
-is given by three contributions:
+This potential was first proposed in :ref:`SMTB-Q_0 <SMTB-Q_0>`.
+Briefly, the energy of metallic-oxygen systems is given by three contributions:
 
 .. math::
 
@@ -208,7 +209,7 @@ For each cations (metal):
 6) Coordination parameter:
 
 * First (:math:`r_{1n}`) and second (:math:`r_{2n}`) neighbor distances
-  in Angstrom
+  in angstroms
 * Divider line
 
 7) Charge initialization mode:
@@ -306,6 +307,12 @@ and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
 
 ----------
 
+.. _SMTB-Q_0:
+
+**(SMTB-Q_0)** A. Hallil, E. Amzallag, S. Landron, R. Tetot,
+Surface Science 605 738-745 (2011);
+R. Tetot, A. Hallil, J. Creuze and I. Braems, EPL, 83 40001 (2008)
+
 .. _SMTB-Q_1:
 
 **(SMTB-Q_1)** N. Salles, O. Politano, E. Amzallag, R. Tetot,

doc/utils/check-styles.py

@@ -227,6 +227,8 @@ for header in headers:
                     register_style(reader,style,info)
                 elif m[0] == 'Region':
                     register_style(region,style,info)
+                elif m[0] == 'GranSubMod':
+                    pass  # ignore GranSubMod styles for now
                 else:
                     print("Skipping over: ",m)
 

doc/utils/requirements.txt

@@ -1,6 +1,6 @@
-Sphinx < 6.0.0
+Sphinx >= 5.0.0, <7.0.0
 sphinxcontrib-spelling
-sphinxcontrib-jquery >=3.0.0
+sphinxcontrib-jquery
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read
 sphinx_tabs
 breathe

doc/utils/sphinx-config/_themes/lammps_theme/__init__.py

@@ -12,7 +12,7 @@ from sphinx.locale import _
 from sphinx.util.logging import getLogger
 
 
-__version__ = '1.1.1'
+__version__ = '1.2.0'
 __version_full__ = __version__
 
 logger = getLogger(__name__)
@@ -40,15 +40,24 @@ def extend_html_context(app, pagename, templatename, context, doctree):
 # See http://www.sphinx-doc.org/en/stable/theming.html#distribute-your-theme-as-a-python-package
 def setup(app):
     if python_version[0] < 3:
-        logger.warning("Python 2 is deprecated with sphinx_rtd_theme, update to Python 3")
+        logger.warning("Python 2 is deprecated with lammps_theme, update to Python 3")
     app.require_sphinx('1.6')
     if sphinx_version <= (2, 0, 0):
-        logger.warning("Sphinx 1.x is deprecated with sphinx_rtd_theme, update to Sphinx 2.x or greater")
+        logger.warning("Sphinx 1.x is deprecated with lammps_theme, update to Sphinx 2.x or greater")
         if not app.config.html_experimental_html5_writer:
-            logger.warning("'html4_writer' is deprecated with sphinx_rtd_theme")
+            logger.warning("'html4_writer' is deprecated with lammps_theme")
     else:
         if app.config.html4_writer:
-            logger.warning("'html4_writer' is deprecated with sphinx_rtd_theme")
+            logger.warning("'html4_writer' is deprecated with lammps_theme")
+
+    # Since Sphinx 6, jquery isn't bundled anymore and we need to ensure that
+    # the sphinxcontrib-jquery extension is enabled.
+    # See: https://dev.readthedocs.io/en/latest/design/sphinx-jquery.html
+    if sphinx_version >= (6, 0, 0):
+        # Documentation of Sphinx guarantees that an extension is added and
+        # enabled at most once.
+        # See: https://www.sphinx-doc.org/en/master/extdev/appapi.html#sphinx.application.Sphinx.setup_extension
+        app.setup_extension("sphinxcontrib.jquery")
 
     # Register the theme that can be referenced without adding a theme path
     app.add_html_theme('lammps_theme', path.abspath(path.dirname(__file__)))

doc/utils/sphinx-config/_themes/lammps_theme/breadcrumbs.html

@@ -22,7 +22,7 @@
 <div role="navigation" aria-label="{{ _('Page navigation') }}">
   <ul class="wy-breadcrumbs">
     {%- block breadcrumbs %}
-      <li><a href="{{ pathto(master_doc) }}" class="icon icon-home"></a></li>
+      <li><a href="{{ pathto(master_doc) }}" class="icon icon-home" aria-label="Home"></a></li>
         {%- for doc in parents %}
           <li class="breadcrumb-item"><a href="{{ doc.link|e }}">{{ doc.title }}</a></li>
         {%- endfor %}

doc/utils/sphinx-config/_themes/lammps_theme/footer.html

@@ -60,4 +60,3 @@
   {%- block extrafooter %} {% endblock %}
 
 </footer>
-

doc/utils/sphinx-config/_themes/lammps_theme/layout.html

@@ -40,14 +40,14 @@
     <link rel="stylesheet" href="{{ pathto(cssfile, 1) }}" type="text/css" />
   {%- endfor -%}
 
-  {#- FAVICON #}
+  {#- FAVICON
-  {%- if favicon %}
+      favicon_url is the only context var necessary since Sphinx 4.
-    {%- if sphinx_version_info < (4, 0) -%}
+      In Sphinx<4, we use favicon but need to prepend path info.
-    <link rel="shortcut icon" href="{{ pathto('_static/' + favicon, 1) }}"/>
+  #}
-    {%- else %}
+  {%- set _favicon_url = favicon_url | default(pathto('_static/' + (favicon or ""), 1)) %}
-    <link rel="shortcut icon" href="{{ favicon_url }}"/>
+  {%- if favicon_url or favicon %}
-    {%- endif %}
+    <link rel="shortcut icon" href="{{ _favicon_url }}"/>
-  {%- endif -%}
+  {%- endif %}
 
   {#- CANONICAL URL (deprecated) #}
   {%- if theme_canonical_url and not pageurl %}
@@ -133,27 +133,20 @@
         <div class="wy-side-nav-search" {% if theme_style_nav_header_background %} style="background: {{theme_style_nav_header_background}}" {% endif %}>
           {%- block sidebartitle %}
 
-          {%- if logo and theme_logo_only %}
+          {# the logo helper function was removed in Sphinx 6 and deprecated since Sphinx 4 #}
-            <a href="{{ pathto(master_doc) }}">
+          {# the master_doc variable was renamed to root_doc in Sphinx 4 (master_doc still exists in later Sphinx versions) #}
-          {%- else %}
+          {%- set _logo_url = logo_url|default(pathto('_static/' + (logo or ""), 1)) %}
-            <a href="{{ pathto(master_doc) }}" class="icon icon-home"> {{ project }}
+          {%- set _root_doc = root_doc|default(master_doc) %}
-          {%- endif %}
+          <a href="{{ pathto(_root_doc) }}"{% if not theme_logo_only %} class="icon icon-home"{% endif %}>
-
+            {% if not theme_logo_only %}{{ project }}{% endif %}
-          {%- if logo %}
+            {%- if logo or logo_url %}
-            {#- Not strictly valid HTML, but it's the only way to display/scale
+              <img src="{{ _logo_url }}" class="logo" alt="{{ _('Logo') }}"/>
-                it properly, without weird scripting or heaps of work
-            #}
-            {%- if sphinx_version_info < (4, 0) -%}
-            <img src="{{ pathto('_static/' + logo, 1) }}" class="logo" alt="{{ _('Logo') }}"/>
-            {%- else %}
-            <img src="{{ logo_url }}" class="logo" alt="{{ _('Logo') }}"/>
             {%- endif %}
-          {%- endif %}
           </a>
 
           {%- if theme_display_version %}
-              <div class="lammps_version">Version: <b>{{ current_version }}</b></div>
+            <div class="lammps_version">Version: <b>{{ current_version }}</b></div>
-              <div class="lammps_release">git info: {{ release }}</div>
+            <div class="lammps_release">git info: {{ release }}</div>
           {%- endif %}
 
           {%- include "searchbox.html" %}

doc/utils/sphinx-config/_themes/lammps_theme/locale/de/LC_MESSAGES/sphinx.po

@@ -1,136 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Tom Kunze <transifex.com@tomabrafix.de>, 2019
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Tom Kunze <transifex.com@tomabrafix.de>, 2019\n"
-"Language-Team: German (https://www.transifex.com/readthedocs/teams/101354/de/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: de\n"
-"Plural-Forms: nplurals=2; plural=(n != 1);\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Auf GitHub bearbeiten"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Auf Bitbucket bearbeiten"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Auf GitLab bearbeiten"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Quelltext anzeigen"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Zurück"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Weiter"
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Build"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Zuletzt aktualisiert am %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Erstellt mit %(sphinx_web)s mit einem"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "bereitgestellt von %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "%(docstitle)s durchsuchen"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Über diese Dokumentation"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Index"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Suche"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Copyright"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Bitte aktiviere JavaScript, um die Suchfunktion zu nutzen."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Suchergebnisse"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Es wurden keine mit deiner Suchanfrage übereinstimmenden Dokumente gefunden."
-" Achte darauf, dass alle Wörter richtig geschrieben sind und dass genug "
-"Kategorien ausgewählt sind."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Dokumentation durchsuchen"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versionen"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Auf Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Projektübersicht"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Builds"

doc/utils/sphinx-config/_themes/lammps_theme/locale/en/LC_MESSAGES/sphinx.po

@@ -8,7 +8,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
 "Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
+"POT-Creation-Date: 2023-02-06 15:36+0100\n"
 "PO-Revision-Date: 2019-07-16 15:43-0600\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language: en\n"
@@ -17,7 +17,7 @@ msgstr ""
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=utf-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
+"Generated-By: Babel 2.11.0\n"
 
 #. This is an ARIA section label for page links, including previous/next page
 #. link and links to GitHub/GitLab/etc.
@@ -126,18 +126,18 @@ msgstr ""
 msgid "Copyright"
 msgstr ""
 
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
+#: sphinx_rtd_theme/layout.html:143
 msgid "Logo"
 msgstr ""
 
 #. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
+#: sphinx_rtd_theme/layout.html:166
 msgid "Navigation menu"
 msgstr ""
 
 #. This is an ARIA section label for the navigation menu that is visible when
 #. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
+#: sphinx_rtd_theme/layout.html:188
 msgid "Mobile navigation menu"
 msgstr ""
 

doc/utils/sphinx-config/_themes/lammps_theme/locale/es/LC_MESSAGES/sphinx.po

@@ -1,169 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Anthony <aj@ohess.org>, 2019
-# Radina Matic <radina.matic@gmail.com>, 2021
-# Leonardo J. Caballero G. <leonardocaballero@gmail.com>, 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Leonardo J. Caballero G. <leonardocaballero@gmail.com>, 2022\n"
-"Language-Team: Spanish (https://www.transifex.com/readthedocs/teams/101354/es/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: es\n"
-"Plural-Forms: nplurals=3; plural=n == 1 ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Editar en GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Editar en Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Editar en GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Ver código fuente de la página"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Anterior"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Siguiente"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Pie de página"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Derechos de autor</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Derechos de autor %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Compilación"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Revisión"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Actualizado por última vez el %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Compilado con %(sphinx_web)s usando un"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "tema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "proporcionado por %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Buscar en %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Sobre esta documentación"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Índice"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Búsqueda"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Derechos de autor"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logotipo"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr ""
-"Por favor, active JavaScript para habilitar la funcionalidad de búsqueda."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Resultados de la búsqueda"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Su búsqueda no coincide con ningún documento. Por favor, asegúrese de que "
-"todas las palabras estén correctamente escritas y que usted haya "
-"seleccionado las suficientes categorías."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Buscar documentos"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versiones"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Descargas"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "En Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Página de Proyecto"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Compilaciones"

doc/utils/sphinx-config/_themes/lammps_theme/locale/et/LC_MESSAGES/sphinx.po

@@ -1,166 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Anthony <aj@ohess.org>, 2020
-# Ivar Smolin <okul@linux.ee>, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Ivar Smolin <okul@linux.ee>, 2021\n"
-"Language-Team: Estonian (https://www.transifex.com/readthedocs/teams/101354/et/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: et\n"
-"Plural-Forms: nplurals=2; plural=(n != 1);\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Muuda GitHubis"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Muuda Bitbucketis"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Muuda GitLabis"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Vaata lehe lähtekoodi"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Eelmine"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Järgmine"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Jalus"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Autoriõigus</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Autoriõigus %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Ehitus"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Redaktsioon"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Viimati uuendatud  %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Ehitatud %(sphinx_web)s'iga,"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "kujundusteema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "on loonud %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Otsi dokumendist %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Nende dokumentide kirjeldused"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Indeks"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Otsing"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Autoriõigus"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Otsimisfunktsiooni lubamiseks aktiveeri palun JavaScript"
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Otsingu tulemused"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Sinu otsingule ei vastanud ükski dokument. Palun veendu, et kõik sisestatud "
-"sõnad on õigesti kirjutatud ja sa oled valikud piisaval hulgal kategooriaid."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Otsi dokumente"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versioonid"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Allalaadimised"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Saidil Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Projekti kodu"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Ehitused"

doc/utils/sphinx-config/_themes/lammps_theme/locale/fa_IR/LC_MESSAGES/sphinx.po

@@ -1,161 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Anthony <aj@ohess.org>, 2021
-# Peyman M., 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Peyman M., 2022\n"
-"Language-Team: Persian (Iran) (https://www.transifex.com/readthedocs/teams/101354/fa_IR/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: fa_IR\n"
-"Plural-Forms: nplurals=2; plural=(n > 1);\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "ویرایش در GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "ویرایش در Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "ویرایش در GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "نمایش متن منبع صفحه"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "پیشین"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "بعدی"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">حق انتشار</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; حق انتشار%(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "ساخت"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "بازبینی"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "آخرین بروز رسانی در %(last_updated)s ."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "ساخته شده با %(sphinx_web)s"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "پوسته"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "تهیّه شده با %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "جستجو در %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "درباره این مستندات"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "فهرست"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "جستجوی"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "کپی رایت"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "آرم"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "لطفاً جاوا اسکریپت را فعّال کنید تا قابلیّت جستجو فعّال شود."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "نتایج جستجو"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"جستجوی شما با هیچ سندی مطابقت نداشت. لطفاً از درستی املای واژگان مطمئن شوید."
-" هم‌چنین بررسی کنید آیا به اندازه کافی دسته بندی انتخاب کرده‌اید."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "جستجوی مستندات"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "نگارش‌ها"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "بارگیری‌ها"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "درباره‌ی خواندن مستندات"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "صفحه خانگی پروژه"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "ساخت‌ها"

doc/utils/sphinx-config/_themes/lammps_theme/locale/fr/LC_MESSAGES/sphinx.po

@@ -1,167 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Anthony <aj@ohess.org>, 2020
-# Radina Matic <radina.matic@gmail.com>, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Radina Matic <radina.matic@gmail.com>, 2021\n"
-"Language-Team: French (https://www.transifex.com/readthedocs/teams/101354/fr/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: fr\n"
-"Plural-Forms: nplurals=3; plural=(n == 0 || n == 1) ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Éditer sur GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Éditer sur Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Éditer sur GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Afficher la source de la page"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Précédent"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Suivant"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Pied de page"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Droits d'auteur</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Droits d'auteur %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Compilation"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Révision"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Dernière mise à jour le %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Compilé avec %(sphinx_web)s en utilisant un"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "thème"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "fourni par %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Rechercher dans %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "À propos de cette documentation"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Index"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Rechercher"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Droits d'auteur"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Activez JavaScript pour accéder à la fonction de recherche."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Résultats de la recherche"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Votre recherche ne correspond à aucun document. Assurez-vous que tous les "
-"mots sont correctement orthographiés et que vous avez sélectionné "
-"suffisamment de catégories."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Rechercher docs"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versions"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Téléchargements"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "À propos de Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Accueil du projet"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Compilations"

doc/utils/sphinx-config/_themes/lammps_theme/locale/hr/LC_MESSAGES/sphinx.po

@@ -1,23 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Ivan Bratović, 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Ivan Bratović, 2022\n"
-"Language-Team: Croatian (https://www.transifex.com/readthedocs/teams/101354/hr/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: hr\n"
-"Plural-Forms: nplurals=3; plural=n%10==1 && n%100!=11 ? 0 : n%10>=2 && n%10<=4 && (n%100<10 || n%100>=20) ? 1 : 2;\n"

doc/utils/sphinx-config/_themes/lammps_theme/locale/hu/LC_MESSAGES/sphinx.po

@@ -1,23 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Balázs Úr, 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Balázs Úr, 2022\n"
-"Language-Team: Hungarian (https://www.transifex.com/readthedocs/teams/101354/hu/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: hu\n"
-"Plural-Forms: nplurals=2; plural=(n != 1);\n"

doc/utils/sphinx-config/_themes/lammps_theme/locale/it/LC_MESSAGES/sphinx.po

@@ -1,192 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Anthony <aj@ohess.org>, 2021
-# Maurizio Paglia <mpaglia0@gmail.com>, 2021
-# albanobattistella <albano_battistella@hotmail.com>, 2022
-# Benjamin Bach <benjaoming@gmail.com>, 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Benjamin Bach <benjaoming@gmail.com>, 2022\n"
-"Language-Team: Italian (https://www.transifex.com/readthedocs/teams/101354/it/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: it\n"
-"Plural-Forms: nplurals=3; plural=n == 1 ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "Naviga tra le pagine"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Modifica su GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Modifica su Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Modifica su GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Visualizza sorgente pagina"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "Naviga sequenzialmente tra le pagine"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Precedente"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Prossimo"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Piè di pagina"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Copyright %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Rev."
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Revisione"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Ultimo aggiornamento il %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Realizzato con %(sphinx_web)s usando un"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "tema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "fornito da %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Cerca in %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Nota sulla documentazione"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Indice"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Ricerca"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Copyright"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "Menu di navigazione"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "Menu navigazione dispositivi mobili"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Devi attivare JavaScript per attivare la funzione di ricerca."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Risultati della ricerca"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"La tua ricerca non ha prodotto nessun risultato. Assicurati di aver scritto "
-"correttamente tutti i termini cercati e di aver selezionato sufficienti "
-"categorie."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Cerca documenti"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versioni"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Downloads"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Riguardo Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Home progetto"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Rev."

doc/utils/sphinx-config/_themes/lammps_theme/locale/lt/LC_MESSAGES/sphinx.po

@@ -1,188 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Tomas Straupis, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Tomas Straupis, 2021\n"
-"Language-Team: Lithuanian (https://www.transifex.com/readthedocs/teams/101354/lt/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: lt\n"
-"Plural-Forms: nplurals=4; plural=(n % 10 == 1 && (n % 100 > 19 || n % 100 < 11) ? 0 : (n % 10 >= 2 && n % 10 <=9) && (n % 100 > 19 || n % 100 < 11) ? 1 : n % 1 != 0 ? 2: 3);\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "Puslapių navigacija"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Keisti GitHub'e"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Keisti Bitbucket'e"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Keisti GitLab'e"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Žiūrėti puslapio šaltinį"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "Puslapių navigacija iš eilės"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Ankstesnis"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Kitas"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Poraštė"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Copyright %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Surinkimas"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Versija"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Atnaujinta %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Surinkta su %(sphinx_web)s naudojant"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "temą"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "pateiktą %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Ieškoti %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Apie šiuos dokumentus"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Indeksas"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Paieška"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Autorių teisės"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "Navigacijos meniu"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "Mobilios navigacijos meniu"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Prašome įjungti JavaScript, kad veiktų paieškos funkcionalumas."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Paieškos rezultatai"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Jūsų paieškai neatitiko nei vienas dokumentas. Prašome įsitikinti, kad visi "
-"žodžiai parašyti teisingai ir kad parinkote pakankamai kategorijų."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Ieškoti dokumentuose"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versijos"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Atsisiuntimai"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Apie Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Projekto namai"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Surinkimai"

doc/utils/sphinx-config/_themes/lammps_theme/locale/nl/LC_MESSAGES/sphinx.po

@@ -1,188 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Jesse Tan, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Jesse Tan, 2021\n"
-"Language-Team: Dutch (https://www.transifex.com/readthedocs/teams/101354/nl/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: nl\n"
-"Plural-Forms: nplurals=2; plural=(n != 1);\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "Paginanavigatie"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Bewerk op GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Bewerk op BitBucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Bewerk op GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Bekijk paginabron"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "Navigatie voor gerelateerde pagina's"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Vorige"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Volgende"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Voettekst"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Copyright %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Bouwresultaat"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Revisie"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Laatste update op %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Gebouwd met %(sphinx_web)s met een"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "thema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "geleverd door %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Zoek binnen %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Over deze documenten"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Index"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Zoek"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Copyright"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "Navigatiemenu"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "Navigatiemenu voor mobiel"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Zet JavaScript aan om de zoekfunctie mogelijk te maken."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Zoekresultaten"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Zoekpoging vond geen documenten. Zorg ervoor dat alle woorden correct zijn "
-"gespeld en dat voldoende categorieën zijn geselecteerd."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Zoek in documentatie"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versies"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Downloads"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Op Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Project Home"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Bouwresultaten"

doc/utils/sphinx-config/_themes/lammps_theme/locale/pl/LC_MESSAGES/sphinx.po

@@ -1,137 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Michal Sniatala, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Michal Sniatala, 2021\n"
-"Language-Team: Polish (https://www.transifex.com/readthedocs/teams/101354/pl/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: pl\n"
-"Plural-Forms: nplurals=4; plural=(n==1 ? 0 : (n%10>=2 && n%10<=4) && (n%100<12 || n%100>14) ? 1 : n!=1 && (n%10>=0 && n%10<=1) || (n%10>=5 && n%10<=9) || (n%100>=12 && n%100<=14) ? 2 : 3);\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Edytuj na GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Edytuj na Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Edytuj na GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Zobacz źródło strony"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Poprzedni"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Następny"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Prawa zastrzeżone</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Prawa zastrzeżone %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Ostatnia aktualizacja %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Zbudowano w %(sphinx_web)s używając"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "dostarczone przez %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Szukaj w %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "O tych dokumentach"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Indeks"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Szukaj"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Prawa zastrzeżone"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr ""
-"Proszę aktywować obsługę JavaScript, aby włączyć funkcję wyszukiwania."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Wyniki wyszukiwania"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Nie znaleziono szukanej frazy. Upewnij się, że wszystkie słowa są napisane "
-"poprawnie i że wybrałeś wystarczającą liczbę kategorii."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Szukaj"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Wersje"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Pobrania"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Na Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Strona projektu"

doc/utils/sphinx-config/_themes/lammps_theme/locale/pt/LC_MESSAGES/sphinx.po

@@ -1,161 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Ana Costa <anacosta.xl@gmail.com>, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Ana Costa <anacosta.xl@gmail.com>, 2021\n"
-"Language-Team: Portuguese (https://www.transifex.com/readthedocs/teams/101354/pt/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: pt\n"
-"Plural-Forms: nplurals=3; plural=(n == 0 || n == 1) ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "Navegação da página"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Editar no GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Editar no Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Editar no GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Ver código-fonte da página"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "Navegação sequencial da página"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Anterior"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Seguinte"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Rodapé"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Revisão"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Última actualização em %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Compilado com %(sphinx_web)s usando um"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "tema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "fornecido por %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Procurar em %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Sobre estes documentos"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Índice"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Pesquisar"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "Menu de navegação"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "Menu de navegação móvel"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Por favor, active o JavaScript para permitir a função de pesquisa."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Resultados de Pesquisa"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"A sua pesquisa não encontrou nenhum documento. Por favor confirme que todas "
-"as palavras estão bem escritas e que selecionou categorias suficientes."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Pesquisar docs"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versões"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Transferências"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "No Read the Docs"

doc/utils/sphinx-config/_themes/lammps_theme/locale/pt_BR/LC_MESSAGES/sphinx.po

@@ -1,191 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Rafael Fontenelle <rffontenelle@gmail.com>, 2021
-# Wellington Uemura <wellingtonuemura@gmail.com>, 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Wellington Uemura <wellingtonuemura@gmail.com>, 2022\n"
-"Language-Team: Portuguese (Brazil) (https://www.transifex.com/readthedocs/teams/101354/pt_BR/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: pt_BR\n"
-"Plural-Forms: nplurals=3; plural=(n == 0 || n == 1) ? 0 : n != 0 && n % 1000000 == 0 ? 1 : 2;\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "Navegação da página"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Editar no GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Editar no Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Editar no GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Ver código-fonte da página"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "Navegação sequencial da página"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Anterior"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Próximo"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Rodapé"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Direitos autorais</a> %(copyright)s."
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Direitos autorais %(copyright)s."
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Compilação"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Revisão"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Última atualização em %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Compilado com %(sphinx_web)s usando um"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "tema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "fornecido por %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Pesquisar em %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Sobre esses documentos"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Índice"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Pesquisar"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Copyright"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "Menu de navegação"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "Menu de navegação móvel"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr ""
-"Por favor, ative JavaScript para habilitar a funcionalidade de pesquisa."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Resultados da pesquisa"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"A sua pesquisa não encontrou nenhum documento correspondente. Verifique se "
-"todas as palavras estão escritas corretamente e se você selecionou "
-"categorias suficientes."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Pesquisar documentos"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versões"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Downloads"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "No Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Página inicial"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Compilações"

doc/utils/sphinx-config/_themes/lammps_theme/locale/ru/LC_MESSAGES/sphinx.po

@@ -1,189 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# lvv83 <vlozhkin83@gmail.com>, 2019
-# Dmitry Shachnev <mitya57@gmail.com>, 2021
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Dmitry Shachnev <mitya57@gmail.com>, 2021\n"
-"Language-Team: Russian (https://www.transifex.com/readthedocs/teams/101354/ru/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: ru\n"
-"Plural-Forms: nplurals=4; plural=(n%10==1 && n%100!=11 ? 0 : n%10>=2 && n%10<=4 && (n%100<12 || n%100>14) ? 1 : n%10==0 || (n%10>=5 && n%10<=9) || (n%100>=11 && n%100<=14)? 2 : 3);\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "Навигация по страницам"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Редактировать на GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Редактировать на BitBucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Редактировать на GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Просмотреть исходный код страницы"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "Навигация по соседним страницам"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Предыдущая"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Следующая"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "Нижняя область"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">Авторские права</a> %(copyright)s. "
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; Авторские права %(copyright)s. "
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Сборка"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Ревизия"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Последний раз обновлено %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Собрано при помощи %(sphinx_web)s с использованием"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "темы,"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "предоставленной %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Поиск в %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Об этих документах"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Алфавитный указатель"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Поиск"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Авторские права"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Логотип"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "Меню навигации"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "Меню навигации для мобильных устройств"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "Активируйте JavaScript, чтобы использовать функционал поиска."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Результаты поиска"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"По Вашему запросу не найдено результатов. Пожалуйста, проверьте, что все "
-"слова написаны правильно, и Вы выбрали нужные категории."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Поиск в документации"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Версии"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Загрузки"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "На Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Домашняя страница проекта"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Сборки"

doc/utils/sphinx-config/_themes/lammps_theme/locale/sphinx.pot

@@ -1,22 +1,22 @@
 # Translations template for sphinx_rtd_theme.
-# Copyright (C) 2022 ORGANIZATION
+# Copyright (C) 2023 ORGANIZATION
 # This file is distributed under the same license as the sphinx_rtd_theme
 # project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2022.
+# FIRST AUTHOR <EMAIL@ADDRESS>, 2023.
 #
 #, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 1.1.1\n"
+"Project-Id-Version: sphinx_rtd_theme 1.2.0rc4\n"
 "Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
+"POT-Creation-Date: 2023-02-06 15:36+0100\n"
 "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
 "Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=utf-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
+"Generated-By: Babel 2.11.0\n"
 
 #. This is an ARIA section label for page links, including previous/next page
 #. link and links to GitHub/GitLab/etc.
@@ -125,18 +125,18 @@ msgstr ""
 msgid "Copyright"
 msgstr ""
 
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
+#: sphinx_rtd_theme/layout.html:143
 msgid "Logo"
 msgstr ""
 
 #. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
+#: sphinx_rtd_theme/layout.html:166
 msgid "Navigation menu"
 msgstr ""
 
 #. This is an ARIA section label for the navigation menu that is visible when
 #. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
+#: sphinx_rtd_theme/layout.html:188
 msgid "Mobile navigation menu"
 msgstr ""
 

doc/utils/sphinx-config/_themes/lammps_theme/locale/sv/LC_MESSAGES/sphinx.po

@@ -1,151 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# Daniel Holmberg <daniel.holmberg97@gmail.com>, 2020
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: Daniel Holmberg <daniel.holmberg97@gmail.com>, 2020\n"
-"Language-Team: Swedish (https://www.transifex.com/readthedocs/teams/101354/sv/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: sv\n"
-"Plural-Forms: nplurals=2; plural=(n != 1);\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "Editera på GitHub"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Editera på Bitbucket"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "Editera på GitLab"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Visa sidkälla"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Tillbaka"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Nästa"
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Bygg"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Ändra"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Senast uppdaterad %(last_updated)s."
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "Gjord med %(sphinx_web)s med hjälp av"
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "tema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "erhållet av %(readthedocs_web)s"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "Sök i %(docstitle)s"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Om dessa dokument"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Index"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Sök"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Upphovsrätt"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr ""
-"Var vänlig och aktivera JavaScript för att möjliggöra sökfunktionaliteten."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Sökresultat"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Din sökning gav inga träffar. Var vänlig och se till att alla ord är rätt "
-"stavade och att du har valt tillräckligt många kategorier."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Sök i dokumentationen"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Versioner"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "Nerladdningar"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "På Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Projekt Hem"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Versioner"

doc/utils/sphinx-config/_themes/lammps_theme/locale/tr/LC_MESSAGES/sphinx.po

@@ -1,143 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# BouRock, 2020
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: BouRock, 2020\n"
-"Language-Team: Turkish (https://www.transifex.com/readthedocs/teams/101354/tr/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: tr\n"
-"Plural-Forms: nplurals=2; plural=(n > 1);\n"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "GitHub'da Düzenle"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "Bitbucket'ta Düzenle"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "GitLab'ta Düzenle"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "Sayfa kaynağını görüntüle"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "Önceki"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "Sonraki"
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "Oluşturma"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "Gözden geçirme"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "Son olarak %(last_updated)s tarihinde güncellendi."
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "tema"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "kullanılarak %(readthedocs_web)s tarafından sağlanmasıyla oluşturuldu"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "%(docstitle)s içinde ara"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "Bu belgeler hakkında"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "Dizin"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "Arama"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "Telif hakkı"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr ""
-"Arama işlevselliğini etkinleştirmek için lütfen JavaScript'i etkinleştirin."
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "Arama Sonuçları"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr ""
-"Aramanız hiçbir belgeyle eşleşmedi. Lütfen tüm kelimelerin doğru "
-"yazıldığından ve yeterli kategori seçtiğinizden emin olun."
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "Belgeleri arayın"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "Sürümler"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "İndirmeler"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "Read the Docs Üzerinde"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "Proje Ana Sayfa"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "Oluşturmalar"

doc/utils/sphinx-config/_themes/lammps_theme/locale/zh_CN/LC_MESSAGES/sphinx.po

@@ -1,191 +0,0 @@
-# English translations for sphinx_rtd_theme.
-# Copyright (C) 2019 ORGANIZATION
-# This file is distributed under the same license as the sphinx_rtd_theme
-# project.
-# FIRST AUTHOR <EMAIL@ADDRESS>, 2019.
-# 
-# Translators:
-# 王赛 <wangsai@bootcss.com>, 2019
-# Anthony <aj@ohess.org>, 2022
-# JY3, 2022
-# 
-msgid ""
-msgstr ""
-"Project-Id-Version: sphinx_rtd_theme 0.4.3.dev0\n"
-"Report-Msgid-Bugs-To: EMAIL@ADDRESS\n"
-"POT-Creation-Date: 2022-11-04 12:02-0700\n"
-"PO-Revision-Date: 2019-07-16 21:44+0000\n"
-"Last-Translator: JY3, 2022\n"
-"Language-Team: Chinese (China) (https://www.transifex.com/readthedocs/teams/101354/zh_CN/)\n"
-"MIME-Version: 1.0\n"
-"Content-Type: text/plain; charset=UTF-8\n"
-"Content-Transfer-Encoding: 8bit\n"
-"Generated-By: Babel 2.10.1\n"
-"Language: zh_CN\n"
-"Plural-Forms: nplurals=1; plural=0;\n"
-
-#. This is an ARIA section label for page links, including previous/next page
-#. link and links to GitHub/GitLab/etc.
-#: sphinx_rtd_theme/breadcrumbs.html:22
-msgid "Page navigation"
-msgstr "页面导航"
-
-#: sphinx_rtd_theme/breadcrumbs.html:37 sphinx_rtd_theme/breadcrumbs.html:39
-msgid "Edit on GitHub"
-msgstr "在 GitHub 上编辑"
-
-#: sphinx_rtd_theme/breadcrumbs.html:44 sphinx_rtd_theme/breadcrumbs.html:46
-msgid "Edit on Bitbucket"
-msgstr "在 Bitbucket 上编辑"
-
-#: sphinx_rtd_theme/breadcrumbs.html:51 sphinx_rtd_theme/breadcrumbs.html:53
-msgid "Edit on GitLab"
-msgstr "在 GitLab 上编辑"
-
-#: sphinx_rtd_theme/breadcrumbs.html:56 sphinx_rtd_theme/breadcrumbs.html:58
-msgid "View page source"
-msgstr "查看页面源码"
-
-#. This is an ARIA section label for sequential page links, such as previous
-#. and next page links.
-#: sphinx_rtd_theme/breadcrumbs.html:67
-msgid "Sequential page navigation"
-msgstr "顺序式页面导航"
-
-#: sphinx_rtd_theme/breadcrumbs.html:69 sphinx_rtd_theme/footer.html:6
-msgid "Previous"
-msgstr "上一页"
-
-#: sphinx_rtd_theme/breadcrumbs.html:72 sphinx_rtd_theme/footer.html:9
-msgid "Next"
-msgstr "下一页"
-
-#. This is an ARIA section label for the footer section of the page.
-#: sphinx_rtd_theme/footer.html:4
-msgid "Footer"
-msgstr "页脚"
-
-#: sphinx_rtd_theme/footer.html:21
-#, python-format
-msgid "&#169; <a href=\"%(path)s\">Copyright</a> %(copyright)s."
-msgstr "&#169; <a href=\"%(path)s\">版权所有</a> %(copyright)s。"
-
-#: sphinx_rtd_theme/footer.html:23
-#, python-format
-msgid "&#169; Copyright %(copyright)s."
-msgstr "&#169; 版权所有 %(copyright)s。"
-
-#. Build is a noun, not a verb
-#: sphinx_rtd_theme/footer.html:30
-msgid "Build"
-msgstr "构建"
-
-#. the phrase "revision" comes from Git, referring to a commit
-#: sphinx_rtd_theme/footer.html:36
-msgid "Revision"
-msgstr "版本"
-
-#: sphinx_rtd_theme/footer.html:41
-#, python-format
-msgid "Last updated on %(last_updated)s."
-msgstr "最后更新时间 %(last_updated)s。"
-
-#. the variable "sphinx_web" is a link to the Sphinx project documentation
-#. with
-#. the text "Sphinx"
-#: sphinx_rtd_theme/footer.html:53
-#, python-format
-msgid "Built with %(sphinx_web)s using a"
-msgstr "利用 %(sphinx_web)s 构建，使用的 "
-
-#. "theme" refers to a theme for Sphinx, which alters the appearance of the
-#. generated documentation
-#: sphinx_rtd_theme/footer.html:55
-msgid "theme"
-msgstr "主题"
-
-#. this is always used as "provided by Read the Docs", and should not imply
-#. Read the Docs is an author of the generated documentation.
-#: sphinx_rtd_theme/footer.html:57
-#, python-format
-msgid "provided by %(readthedocs_web)s"
-msgstr "由 %(readthedocs_web)s 开发"
-
-#: sphinx_rtd_theme/layout.html:97
-#, python-format
-msgid "Search within %(docstitle)s"
-msgstr "在 %(docstitle)s 中搜索"
-
-#: sphinx_rtd_theme/layout.html:105
-msgid "About these documents"
-msgstr "关于此文档"
-
-#: sphinx_rtd_theme/layout.html:108
-msgid "Index"
-msgstr "索引"
-
-#: sphinx_rtd_theme/layout.html:111 sphinx_rtd_theme/search.html:11
-msgid "Search"
-msgstr "搜索"
-
-#: sphinx_rtd_theme/layout.html:114
-msgid "Copyright"
-msgstr "版权所有"
-
-#: sphinx_rtd_theme/layout.html:147 sphinx_rtd_theme/layout.html:149
-msgid "Logo"
-msgstr "Logo"
-
-#. This is an ARIA section label for the main navigation menu
-#: sphinx_rtd_theme/layout.html:173
-msgid "Navigation menu"
-msgstr "导航菜单"
-
-#. This is an ARIA section label for the navigation menu that is visible when
-#. viewing the page on mobile devices
-#: sphinx_rtd_theme/layout.html:195
-msgid "Mobile navigation menu"
-msgstr "移动版导航菜单"
-
-#: sphinx_rtd_theme/search.html:31
-msgid "Please activate JavaScript to enable the search functionality."
-msgstr "请启用 JavaScript 以便使用搜索功能"
-
-#. Search is a noun, not a verb
-#: sphinx_rtd_theme/search.html:39
-msgid "Search Results"
-msgstr "搜索结果"
-
-#: sphinx_rtd_theme/search.html:41
-msgid ""
-"Your search did not match any documents. Please make sure that all words are"
-" spelled correctly and that you've selected enough categories."
-msgstr "您的搜索没有匹配到任何文档。请确保所有单词拼写正确，并选择了足够多的类别。"
-
-#: sphinx_rtd_theme/searchbox.html:4
-msgid "Search docs"
-msgstr "搜索文档"
-
-#: sphinx_rtd_theme/versions.html:3 sphinx_rtd_theme/versions.html:11
-msgid "Versions"
-msgstr "版本"
-
-#: sphinx_rtd_theme/versions.html:17
-msgid "Downloads"
-msgstr "下载"
-
-#. The phrase "Read the Docs" is not translated
-#: sphinx_rtd_theme/versions.html:24
-msgid "On Read the Docs"
-msgstr "托管于 Read the Docs"
-
-#: sphinx_rtd_theme/versions.html:26
-msgid "Project Home"
-msgstr "项目主页"
-
-#: sphinx_rtd_theme/versions.html:29
-msgid "Builds"
-msgstr "构建"
-
-#~ msgid "Docs"
-#~ msgstr "文档"

doc/utils/sphinx-config/_themes/lammps_theme/searchbox.html

@@ -1,7 +1,7 @@
 {%- if 'singlehtml' not in builder %}
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="{{ pathto('search') }}" method="get">
-    <input type="text" name="q" placeholder="{{ _('Search docs') }}" />
+    <input type="text" name="q" placeholder="{{ _('Search docs') }}" aria-label="{{ _('Search docs') }}" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
   </form>

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

@@ -35,6 +35,9 @@ LAMMPS_DOXYGEN_XML_DIR = '@DOXYGEN_XML_DIR@'
 #sys.path.insert(0, os.path.abspath('.'))
 sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext'))
 
+# add lammps_theme
+sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'utils', 'sphinx-config', '_themes'))
+
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -47,6 +50,7 @@ extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.imgmath',
     'sphinx.ext.autodoc',
+    'lammps_theme',
     'sphinxcontrib.jquery',
     'sphinxfortran.fortran_domain',
     'sphinx_tabs.tabs',
@@ -120,7 +124,7 @@ git_commit = get_git_commit()
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+language = 'en'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:

doc/utils/sphinx-config/false_positives.txt

@@ -355,6 +355,7 @@ bpls
 bpm
 BPM
 br
+Braems
 Branduardi
 Branicio
 brennan
@@ -589,6 +590,7 @@ createAtoms
 CreateIDs
 crespi
 Crespi
+Creuze
 Critchley
 crossterm
 Crowson
@@ -1346,6 +1348,7 @@ Haak
 Hafskjold
 halfstepback
 halgren
+Hallil
 Halperin
 Halver
 Hamaker

examples/COUPLE/README

@@ -33,7 +33,6 @@ These are the sub-directories included in this directory:
 simple              simple example of driver code calling LAMMPS as a lib
 multiple            example of driver code calling multiple instances of LAMMPS
 plugin              example for loading LAMMPS at runtime from a shared library
-lammps_quest        MD with quantum forces, coupling to Quest DFT code
 lammps_spparks      grain-growth Monte Carlo with strain via MD,
                     coupling to SPPARKS kinetic MC code
 library             collection of useful inter-code communication routines

examples/COUPLE/lammps_quest/Makefile.g++

@@ -1,47 +0,0 @@
-# Makefile for MD with quantum forces via LAMMPS <-> Quest coupling
-
-SHELL = /bin/sh
-
-# System-specific settings
-
-LAMMPS =	/home/sjplimp/lammps
-
-CC =		g++
-CCFLAGS =	-g -O -DMPICH_IGNORE_CXX_SEEK -I../library
-DEPFLAGS =	-M
-LINK =		g++
-LINKFLAGS =	-g -O -L../library -L${LAMMPS}/src
-USRLIB =	-lcouple -llammps_g++
-SYSLIB =	-lfftw -lmpich -lpthread
-ARCHIVE =	ar
-ARFLAGS =	-rc
-SIZE =		size
-
-# Files
-
-EXE = 	lmpqst
-SRC =	$(wildcard *.cpp)
-INC =	$(wildcard *.h)
-OBJ = 	$(SRC:.cpp=.o)
-
-# Targets
-
-$(EXE):	$(OBJ)
-	$(LINK) $(LINKFLAGS) $(OBJ) $(USRLIB) $(SYSLIB) -o $(EXE)
-	$(SIZE) $(EXE)
-
-clean:
-	rm $(EXE) *.o
-
-# Compilation rules
-
-%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $<
-
-%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@
-
-# Individual dependencies
-
-DEPENDS = $(OBJ:.o=.d)
-include $(DEPENDS)

examples/COUPLE/lammps_quest/README

@@ -1,70 +0,0 @@
-IMPORTANT NOTE: This example has not been updated since 2014,
-so it is not likely to work anymore out of the box.  There have
-been changes to LAMMPS and its library interface that would need
-to be applied. Please see the manual for the documentation of
-the library interface.
-
-This directory has an application that runs classical MD via LAMMPS,
-but uses quantum forces calculated by the Quest DFT (density
-functional) code in place of the usual classical MD forces calculated
-by a pair style in LAMMPS.
-
-lmpqst.cpp          main program
-                    it links LAMMPS as a library
-                    it invokes Quest as an executable
-in.lammps           LAMMPS input script, without the run command
-si_111.in           Quest input script for an 8-atom Si unit cell
-lmppath.h           contains path to LAMMPS home directory
-qstexe.h            contains full pathname to Quest executable
-
-After editing the Makefile, lmppath.h, and qstexe.h to make them
-suitable for your box, type:
-
-make -f Makefile.g++
-
-and you should get the lmpqst executable.
-
-NOTE: To run this coupled application, you must of course, have Quest
-built on your system.  It's WWW site is http://dft.sandia.gov/Quest.
-It is not an open-source code, buy you can contact its authors to
-obtain a copy.
-
-You can run lmpqst in serial or parallel as:
-
-% lmpqst Niter in.lammps in.quest
-% mpirun -np 4 lmpqst Niter in.lammps in.quest
-
-where
-
-Niter = # of MD iterations
-in.lammps = LAMMPS input script
-in.quest = Quest input script
-
-The log files are for this run:
-
-% lmpqst 10 in.lammps si_111.in
-
-This application is an example of a coupling where the driver code
-(lmpqst) runs one code (LAMMPS) as an outer code and facilitates it
-calling the other code (Quest) as an inner code.  Specifically, the
-driver (lmpqst) invokes one code (LAMMPS) to perform its timestep
-loop, and grabs information from the other code (Quest) during its
-timestep.  This is done in LAMMPS using the fix external command,
-which makes a "callback" to the driver application (lmpqst), which in
-turn invokes Quest with new atom coordinates, lets Quest compute
-forces, and returns those forces to the LAMMPS fix external.
-
-The driver code launches LAMMPS in parallel.  But Quest is only run on
-a single processor.  It would be possible to change this by using a
-parallel build of Quest.
-
-Since Quest does not currently have a library interface, the driver
-code interfaces with Quest via input and output files.
-
-Note that essentially 100% of the run time for this coupled
-application is spent in Quest, as the quantum calculation of forces
-dominates the calculation.
-
-You can look at the log files in the directory to see sample LAMMPS
-output for this simulation.  Dump files produced by LAMMPS are stored
-as dump.md.

examples/COUPLE/lammps_quest/in.lammps

@@ -1,20 +0,0 @@
-# LAMMPS input for coupling MD/Quantum
-
-units		metal
-dimension	3
-atom_style	atomic
-atom_modify	sort 0 0.0
-
-lattice		diamond 5.43
-region		box block 0 1 0 1 0 1
-create_box	1 box
-create_atoms	1 box
-mass		1 28.08
-
-velocity	all create 300.0 87293 loop geom
-
-fix		1 all nve
-fix		2 all external pf/callback 1 1
-
-dump		1 all custom 1 dump.md id type x y z fx fy fz
-thermo		1

examples/COUPLE/lammps_quest/lmppath.h

@@ -1 +0,0 @@
-#define LMPPATH /home/sjplimp/lammps 

examples/COUPLE/lammps_quest/lmpqst.cpp

@@ -1,270 +0,0 @@
-// lmpqst = umbrella driver to couple LAMMPS + Quest
-//          for MD using quantum forces
-
-// Syntax: lmpqst Niter in.lammps in.quest
-//         Niter = # of MD iterations
-//         in.lammps = LAMMPS input script
-//         in.quest = Quest input script
-
-#include <mpi.h>
-#include <cstdio>
-#include <cstdlib>
-#include <cstring>
-#include "stdint.h"
-
-#include "many2one.h"
-#include "one2many.h"
-#include "files.h"
-#include "memory.h"
-#include "error.h"
-
-#define QUOTE_(x) #x
-#define QUOTE(x) QUOTE_(x)
-
-#include "lmppath.h"
-#include QUOTE(LMPPATH/src/lammps.h)
-#include QUOTE(LMPPATH/src/library.h)
-#include QUOTE(LMPPATH/src/input.h)
-#include QUOTE(LMPPATH/src/modify.h)
-#include QUOTE(LMPPATH/src/fix.h)
-#include QUOTE(LMPPATH/src/fix_external.h)
-
-#include "qstexe.h"
-
-using namespace LAMMPS_NS;
-
-#define ANGSTROM_per_BOHR 0.529
-#define EV_per_RYDBERG 13.6056923
-
-void quest_callback(void *, bigint, int, int *, double **, double **);
-
-struct Info {
-  int me;
-  Memory *memory;
-  LAMMPS *lmp;
-  char *quest_input;
-};
-
-/* ---------------------------------------------------------------------- */
-
-int main(int narg, char **arg)
-{
-  int n;
-  char str[128];
-
-  // setup MPI
-
-  MPI_Init(&narg,&arg);
-  MPI_Comm comm = MPI_COMM_WORLD;
-
-  int me,nprocs;
-  MPI_Comm_rank(comm,&me);
-  MPI_Comm_size(comm,&nprocs);
-
-  Memory *memory = new Memory(comm);
-  Error *error = new Error(comm);
-
-  // command-line args
-
-  if (narg != 4) error->all("Syntax: lmpqst Niter in.lammps in.quest");
-
-  int niter = atoi(arg[1]);
-  n = strlen(arg[2]) + 1;
-  char *lammps_input = new char[n];
-  strcpy(lammps_input,arg[2]);
-  n = strlen(arg[3]) + 1;
-  char *quest_input = new char[n];
-  strcpy(quest_input,arg[3]);
-
-  // instantiate LAMMPS
-
-  LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
-
-  // create simulation in LAMMPS from in.lammps
-
-  lmp->input->file(lammps_input);
-
-  // make info available to callback function
-
-  Info info;
-  info.me = me;
-  info.memory = memory;
-  info.lmp = lmp;
-  info.quest_input = quest_input;
-
-  // set callback to Quest inside fix external
-  // this could also be done thru Python, using a ctypes callback
-
-  int ifix = lmp->modify->find_fix("2");
-  FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
-  fix->set_callback(quest_callback,&info);
-
-  // run LAMMPS for Niter
-  // each time it needs forces, it will invoke quest_callback
-
-  sprintf(str,"run %d",niter);
-  lmp->input->one(str);
-
-  // clean up
-
-  delete lmp;
-
-  delete memory;
-  delete error;
-
-  delete [] lammps_input;
-  delete [] quest_input;
-
-  MPI_Finalize();
-}
-
-/* ----------------------------------------------------------------------
-   callback to Quest with atom IDs and coords from each proc
-   invoke Quest to compute forces, load them into f for LAMMPS to use
-   f can be NULL if proc owns no atoms
-------------------------------------------------------------------------- */
-
-void quest_callback(void *ptr, bigint ntimestep,
-		    int nlocal, int *id, double **x, double **f)
-{
-  int i,j;
-  char str[128];
-
-  Info *info = (Info *) ptr;
-
-  // boxlines = LAMMPS box size converted into Quest lattice vectors
-
-  char **boxlines = NULL;
-  if (info->me == 0) {
-    boxlines = new char*[3];
-    for (i = 0; i < 3; i++) boxlines[i] = new char[128];
-  }
-
-  double boxxlo = *((double *) lammps_extract_global(info->lmp,"boxxlo"));
-  double boxxhi = *((double *) lammps_extract_global(info->lmp,"boxxhi"));
-  double boxylo = *((double *) lammps_extract_global(info->lmp,"boxylo"));
-  double boxyhi = *((double *) lammps_extract_global(info->lmp,"boxyhi"));
-  double boxzlo = *((double *) lammps_extract_global(info->lmp,"boxzlo"));
-  double boxzhi = *((double *) lammps_extract_global(info->lmp,"boxzhi"));
-  double boxxy = *((double *) lammps_extract_global(info->lmp,"xy"));
-  double boxxz = *((double *) lammps_extract_global(info->lmp,"xz"));
-  double boxyz = *((double *) lammps_extract_global(info->lmp,"yz"));
-
-  double xprd = (boxxhi-boxxlo)/ANGSTROM_per_BOHR;
-  double yprd = (boxyhi-boxylo)/ANGSTROM_per_BOHR;
-  double zprd = (boxzhi-boxzlo)/ANGSTROM_per_BOHR;
-  double xy = boxxy/ANGSTROM_per_BOHR;
-  double xz = boxxz/ANGSTROM_per_BOHR;
-  double yz = boxyz/ANGSTROM_per_BOHR;
-
-  if (info->me == 0) {
-    sprintf(boxlines[0],"%g %g %g\n",xprd,0.0,0.0);
-    sprintf(boxlines[1],"%g %g %g\n",xy,yprd,0.0);
-    sprintf(boxlines[2],"%g %g %g\n",xz,yz,zprd);
-  }
-
-  // xlines = x for atoms on each proc converted to text lines
-  // xlines is suitable for insertion into Quest input file
-  // convert LAMMPS Angstroms to Quest bohr
-  
-  int natoms;
-  MPI_Allreduce(&nlocal,&natoms,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD);
-
-  Many2One *lmp2qst = new Many2One(MPI_COMM_WORLD);
-  lmp2qst->setup(nlocal,id,natoms);
-
-  char **xlines = NULL;
-  double **xquest = NULL;
-  if (info->me == 0) {
-    xquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:xquest");
-    xlines = new char*[natoms];
-    for (i = 0; i < natoms; i++) xlines[i] = new char[128];
-  }
-
-  if (info->me == 0) lmp2qst->gather(&x[0][0],3,&xquest[0][0]);
-  else lmp2qst->gather(&x[0][0],3,NULL);
-
-  if (info->me == 0) {
-    for (i = 0; i < natoms; i++) {
-      xquest[i][0] /= ANGSTROM_per_BOHR;
-      xquest[i][1] /= ANGSTROM_per_BOHR;
-      xquest[i][2] /= ANGSTROM_per_BOHR;
-    }
-    for (i = 0; i < natoms; i++) {
-      sprintf(xlines[i],"%d %d %g %g %g\n",i+1,1,
-	      xquest[i][0],xquest[i][1],xquest[i][2]);
-    }
-  }
-
-  // one-processor tasks:
-  // whack all lcao.* files
-  // cp quest_input to lcao.in
-  // replace atom coords section of lcao.in with new atom coords
-  // run Quest on one proc, save screen output to file
-  // flines = atom forces extracted from Quest screen file
-  // fquest = atom forces
-  // convert Quest Ryd/bohr to LAMMPS eV/Angstrom
-  
-  char **flines = NULL;
-  double **fquest = NULL;
-  if (info->me == 0) {
-    fquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:fquest");
-    flines = new char*[natoms];
-    for (i = 0; i < natoms; i++) flines[i] = new char[128];
-  }
-
-  if (info->me == 0) {
-    system("rm lcao.*");
-    sprintf(str,"cp %s lcao.in",info->quest_input);
-    system(str);
-    sprintf(str,"cp %s lcao.x",QUOTE(QUEST));
-    system(str);
-    replace("lcao.in","primitive lattice vectors",3,boxlines);
-    replace("lcao.in","atom, type, position vector",natoms,xlines);
-    system("lcao.x > lcao.screen");
-    extract("lcao.screen","atom       x force          "
-	    "y force          z force",natoms,flines);
-    
-    int itmp;
-    for (i = 0; i < natoms; i++)
-      sscanf(flines[i],"%d %lg %lg %lg",&itmp,
-	     &fquest[i][0],&fquest[i][1],&fquest[i][2]);
-
-    for (i = 0; i < natoms; i++) {
-      fquest[i][0] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
-      fquest[i][1] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
-      fquest[i][2] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
-    }
-  }
-
-  // convert fquest on one proc into f for atoms on each proc
-
-  One2Many *qst2lmp = new One2Many(MPI_COMM_WORLD);
-  qst2lmp->setup(natoms,nlocal,id);
-  double *fvec = NULL;
-  if (f) fvec = &f[0][0];
-  if (info->me == 0) qst2lmp->scatter(&fquest[0][0],3,fvec);
-  else qst2lmp->scatter(NULL,3,fvec);
-
-  // clean up
-  // some data only exists on proc 0
-
-  delete lmp2qst;
-  delete qst2lmp;
-
-  info->memory->destroy_2d_double_array(xquest);
-  info->memory->destroy_2d_double_array(fquest);
-
-  if (boxlines) {
-    for (i = 0; i < 3; i++) delete [] boxlines[i];
-    delete [] boxlines;
-  }
-  if (xlines) {
-    for (i = 0; i < natoms; i++) delete [] xlines[i];
-    delete [] xlines;
-  }
-  if (flines) {
-    for (i = 0; i < natoms; i++) delete [] flines[i];
-    delete [] flines;
-  }
-}

examples/COUPLE/lammps_quest/log.lammps.1

@@ -1,58 +0,0 @@
-LAMMPS (20 Sep 2010)
-# LAMMPS input for coupling MD/Quantum
-
-units		metal
-dimension	3
-atom_style	atomic
-atom_modify	sort 0 0.0
-
-lattice		diamond 5.43
-Lattice spacing in x,y,z = 5.43 5.43 5.43
-region		box block 0 1 0 1 0 1
-create_box	1 box
-Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
-  1 by 1 by 1 processor grid
-create_atoms	1 box
-Created 8 atoms
-mass		1 28.08
-
-velocity	all create 300.0 87293 loop geom
-
-fix		1 all nve
-fix		2 all external
-
-dump		1 all custom 1 dump.md id type x y z fx fy fz
-thermo		1
-run 10
-Memory usage per processor = 1.25982 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          300            0            0    0.2714463    1810.9378 
-       1    298.22165            0            0   0.26983722    1800.2029 
-       2     293.2839            0            0   0.26536943    1770.3964 
-       3    286.18537            0            0   0.25894654    1727.5464 
-       4    277.61576            0            0   0.25119258    1675.8163 
-       5     267.3325            0            0   0.24188807    1613.7418 
-       6    254.94702            0            0   0.23068142    1538.9774 
-       7    240.91176            0            0   0.21798202    1454.2541 
-       8    226.27996            0            0   0.20474287    1365.9298 
-       9     212.1059            0            0   0.19191788    1280.3687 
-      10    199.27609            0            0   0.18030919     1202.922 
-Loop time of 80.663 on 1 procs for 10 steps with 8 atoms
-
-Pair  time (%) = 0 (0)
-Neigh time (%) = 0 (0)
-Comm  time (%) = 4.91142e-05 (6.08882e-05)
-Outpt time (%) = 0.00111485 (0.0013821)
-Other time (%) = 80.6618 (99.9986)
-
-Nlocal:    8 ave 8 max 8 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    10 ave 10 max 10 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
-
-Total # of neighbors = 0
-Ave neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0

examples/COUPLE/lammps_quest/log.lammps.4

@@ -1,58 +0,0 @@
-LAMMPS (20 Sep 2010)
-# LAMMPS input for coupling MD/Quantum
-
-units		metal
-dimension	3
-atom_style	atomic
-atom_modify	sort 0 0.0
-
-lattice		diamond 5.43
-Lattice spacing in x,y,z = 5.43 5.43 5.43
-region		box block 0 1 0 1 0 1
-create_box	1 box
-Created orthogonal box = (0 0 0) to (5.43 5.43 5.43)
-  1 by 2 by 2 processor grid
-create_atoms	1 box
-Created 8 atoms
-mass		1 28.08
-
-velocity	all create 300.0 87293 loop geom
-
-fix		1 all nve
-fix		2 all external
-
-dump		1 all custom 1 dump.md id type x y z fx fy fz
-thermo		1
-run 10
-Memory usage per processor = 1.25928 Mbytes
-Step Temp E_pair E_mol TotEng Press 
-       0          300            0            0    0.2714463    1810.9378 
-       1    298.22166            0            0   0.26983722    1800.2029 
-       2    293.28391            0            0   0.26536944    1770.3964 
-       3    286.18538            0            0   0.25894655    1727.5464 
-       4    277.61578            0            0   0.25119259    1675.8164 
-       5    267.33252            0            0   0.24188809    1613.7419 
-       6    254.94703            0            0   0.23068143    1538.9774 
-       7    240.91175            0            0   0.21798202     1454.254 
-       8    226.27997            0            0   0.20474287    1365.9299 
-       9    212.10594            0            0   0.19191791    1280.3689 
-      10    199.27613            0            0   0.18030923    1202.9223 
-Loop time of 79.8256 on 4 procs for 10 steps with 8 atoms
-
-Pair  time (%) = 0 (0)
-Neigh time (%) = 0 (0)
-Comm  time (%) = 0.000365376 (0.000457718)
-Outpt time (%) = 0.00169969 (0.00212925)
-Other time (%) = 79.8236 (99.9974)
-
-Nlocal:    2 ave 2 max 2 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Nghost:    5 ave 5 max 5 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-Neighs:    0 ave 0 max 0 min
-Histogram: 4 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 0
-Ave neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0

examples/COUPLE/lammps_quest/qstexe.h

@@ -1 +0,0 @@
-#define QUEST /home/sjplimp/csrf/quest/src/lcao.x 

examples/COUPLE/lammps_quest/si_111.in

@@ -1,161 +0,0 @@
-do setup
-do iters
-do force
-no relax
-setup data
-title
-Si 1x1x1 unit cell
-functional
-PBE
-dimensions of system (0=cluster ... 3=bulk)
-3
-primitive lattice vectors
-10.261212 0.000000 0.000000
-0.000000 10.261212 0.000000
-0.000000 0.000000 10.261212
-grid dimensions
-10 10 10
-atom types
-1
-type number, label:
- 1 Si_pbe
-notes5
- Originally constructed by Peter A. Schultz, 12Apr01
- potential generated by new Hamann program PUNSLDX
- Cite use with: D.R. Hamann, unpublished.
- Potential: "standard" setting out to l=2
- Basis: amended Jun05 for better (2d/1d not 1d/1d) d-function
-effective nuclear charge (s2p2 to 10.0)
-  4.00000000d+00
-pseudopotentials: Lmax, and effective gaussian range
-  2   0.86000000d+00
-functional type used in generating potential:
-PBE
-radial mesh: number of points for local and non-local pot integrals
-  80  67
-mesh points for nuclear potential;  ham2dh
-     0.02500000  0.02696978  0.02909477  0.03138719  0.03386023  0.03652812
-     0.03940622  0.04251109  0.04586060  0.04947402  0.05337215  0.05757741
-     0.06211402  0.06700807  0.07228773  0.07798338  0.08412779  0.09075634
-     0.09790716  0.10562140  0.11394345  0.12292121  0.13260635  0.14305458
-     0.15432605  0.16648562  0.17960325  0.19375443  0.20902061  0.22548964
-     0.24325628  0.26242278  0.28309943  0.30540522  0.32946852  0.35542780
-     0.38343245  0.41364362  0.44623518  0.48139466  0.51932441  0.56024270
-     0.60438500  0.65200533  0.70337773  0.75879783  0.81858456  0.88308197
-     0.95266121  1.02772271  1.10869840  1.19605428  1.29029305  1.39195702
-     1.50163124  1.61994684  1.74758469  1.88527930  2.03382306  2.19407079
-     2.36694466  2.55343950  2.75462852  2.97166951  3.20581145  3.45840177
-     3.73089402  4.02485632  4.34198031  4.68409093  5.05315693  5.45130215
-     5.88081777  6.34417553  6.84404189  7.38329340  7.96503329  8.59260927
-     9.26963282 10.00000000
-radwts: weights for radial points
-     0.00189603  0.00204542  0.00220659  0.00238045  0.00256800  0.00277034
-     0.00298862  0.00322410  0.00347813  0.00375218  0.00404781  0.00436675
-     0.00471081  0.00508198  0.00548240  0.00591436  0.00638036  0.00688308
-     0.00742541  0.00801047  0.00864162  0.00932251  0.01005704  0.01084945
-     0.01170429  0.01262649  0.01362135  0.01469459  0.01585240  0.01710143
-     0.01844888  0.01990249  0.02147064  0.02316234  0.02498733  0.02695611
-     0.02908002  0.03137128  0.03384307  0.03650961  0.03938625  0.04248955
-     0.04583736  0.04944895  0.05334510  0.05754823  0.06208254  0.06697411
-     0.07225109  0.07794385  0.08408515  0.09071034  0.09785753  0.10556786
-     0.11388570  0.12285891  0.13253914  0.14298208  0.15424783  0.16640123
-     0.17951222  0.19365623  0.20891467  0.22537535  0.24313298  0.26228977
-     0.28295594  0.30525043  0.32930153  0.35524766  0.38323811  0.41343397
-     0.44600900  0.48115067  0.51906119  0.55995874  0.60407867  0.65167486
-     0.70302122  0.75841323
-non-local potential: l,potential*integration weight
- 0   0.62022930  0.62128855  0.62243016  0.62366033  0.62498568  0.62641328
-     0.62795061  0.62960563  0.63138673  0.63330275  0.63536294  0.63757692
-     0.63995464  0.64250630  0.64524218  0.64817253  0.65130735  0.65465605
-     0.65822713  0.66202767  0.66606269  0.67033437  0.67484108  0.67957602
-     0.68452576  0.68966817  0.69497006  0.70038419  0.70584566  0.71126756
-     0.71653578  0.72150290  0.72598113  0.72973436  0.73246932  0.73382636
-     0.73337030  0.73058243  0.72485505  0.71549107  0.70171167  0.68267654
-     0.65752236  0.62542611  0.58570073  0.53792896  0.48213811  0.41900888
-     0.35009536  0.27800640  0.20646172  0.14009458  0.08384960  0.04186877
-     0.01596164  0.00423035  0.00115036  0.00066636  0.00047879  0.00029939
-     0.00016329  0.00007995  0.00003517  0.00001362  0.00000445  0.00000111
-     0.00000016  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-     0.00000000  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-     0.00000000  0.00000000
-non-local potential: l,potential*integration weight
- 1   0.59551624  0.59463303  0.59368033  0.59265268  0.59154422  0.59034862
-     0.58905906  0.58766819  0.58616811  0.58455033  0.58280567  0.58092430
-     0.57889565  0.57670833  0.57435015  0.57180802  0.56906791  0.56611482
-     0.56293268  0.55950435  0.55581158  0.55183493  0.54755377  0.54294628
-     0.53798942  0.53265896  0.52692951  0.52077458  0.51416671  0.50707751
-     0.49947790  0.49133817  0.48262822  0.47331766  0.46337588  0.45277197
-     0.44147437  0.42945016  0.41666374  0.40307468  0.38863443  0.37328165
-     0.35693601  0.33949042  0.32080256  0.30068740  0.27891443  0.25521609
-     0.22931791  0.20100526  0.17024474  0.13737521  0.10336405  0.07007167
-     0.04035673  0.01767907  0.00470635  0.00076638  0.00047880  0.00029939
-     0.00016329  0.00007995  0.00003517  0.00001362  0.00000445  0.00000111
-     0.00000016  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-     0.00000000  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-     0.00000000  0.00000000
-non-local potential: l,potential*integration weight
- 2   0.56305372  0.55961728  0.55591134  0.55191498  0.54760572  0.54295941
-     0.53795013  0.53255008  0.52672947  0.52045641  0.51369682  0.50641433
-     0.49857022  0.49012333  0.48103004  0.47124429  0.46071759  0.44939919
-     0.43723624  0.42417413  0.41015690  0.39512792  0.37903070  0.36181001
-     0.34341340  0.32379300  0.30290805  0.28072780  0.25723539  0.23243242
-     0.20634465  0.17902876  0.15058041  0.12114359  0.09092117  0.06018665
-     0.02929636 -0.00129833 -0.03104046 -0.05926034 -0.08517498 -0.10789810
-    -0.12646610 -0.13988656 -0.14721657 -0.14767751 -0.14080976 -0.12666296
-    -0.10600305 -0.08049270 -0.05276798 -0.02629475 -0.00486427  0.00837657
-     0.01228139  0.00892332  0.00342796  0.00074936  0.00047880  0.00029939
-     0.00016329  0.00007995  0.00003517  0.00001362  0.00000445  0.00000111
-     0.00000016  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-     0.00000000  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-     0.00000000  0.00000000
-number of radial functions  **** Si PBE Ham-II basis 20Feb01-PAS ****
- 5
-angular momentum, number of alphas
- 0  4
-alphas - s - 4s/2/4s407 (bulk Si dzp Eopt+reopt c1)
-  0.10460000d+00  0.27226300d+00  1.30050800d+00  2.60103000d+00
-wave function coefficients
-  0.20995300d+00  0.55978200d+00 -0.99128200d+00  0.33487100d+00
-angular momentum, number of alphas
- 1  3
-alphas - p - 3p/2/3p492 (bulk Si dzp Eopt + reopt c1)
-  0.09424100d+00  0.31767900d+00  1.56114500d+00
-wave function coefficients
-  0.06761600d+00  0.31821200d+00 -0.06638300d+00
-angular momentum, number of alphas
- 0  1
-alphas - s - second zeta s polarization
-  0.10460000d+00
-wave function coefficients
-  1.00000000d+00
-angular momentum, number of alphas
- 1  1
-alphas - p - second zeta p polarization
-  0.09424100d+00
-wave function coefficients
-  1.00000000d+00
-angular momentum, number of alphas
- 2  2
-alphas - d - angular polarization (dzp Eopt)
-  0.32000000d+00  1.40000000d+00
-wave function coefficients
-  0.31557000d+00  1.00000000d+00
-shell occupancies for this silicon, Si: s(2.00)p(2.00)
-     2.00000000  2.00000000  0.00000000  0.00000000  0.00000000  0.00000000
-end atom file
-number of atoms in unit cell
-8
-atom, type, position vector
-1 1   0.0000000000   0.0000000000   0.0000000000
-2 1   5.1306060590   5.1306060590   0.0000000000
-3 1   5.1306060590   0.0000000000   5.1306060590
-4 1   0.0000000000   5.1306060590   5.1306060590
-5 1   2.5653030295   2.5653030295   2.5653030295
-6 1   7.6959090885   7.6959090885   2.5653030295
-7 1   7.6959090885   2.5653030295   7.6959090885
-8 1   2.5653030295   7.6959090885   7.6959090885
-kgrid
-0 0 0
-end setup phase data
-run phase input data
-end of run phase data

examples/COUPLE/lammps_spparks/Makefile.mpi

@@ -2,18 +2,20 @@
 
 SHELL = /bin/sh
 
+# Paths to your local LAMMPS and SPPARKS home directories
+
+LAMMPS =	/home/sjplimp/lammps/git
+SPPARKS =	/home/sjplimp/spparks/git
+
 # System-specific settings
 
-LAMMPS =	/home/sjplimp/lammps
+CC =		mpicxx
-SPPARKS =	/home/sjplimp/spparks
-
-CC =		g++
 CCFLAGS =	-g -O -DMPICH_IGNORE_CXX_SEEK -I../library
 DEPFLAGS =	-M
-LINK =		g++
+LINK =		mpicxx
 LINKFLAGS =	-g -O -L../library -L${LAMMPS}/src -L${SPPARKS}/src
-USRLIB =	-lcouple -llmp_g++ -lspk_g++ 
+USRLIB =	-lcouple -llammps_mpi -lspparks_mpi 
-SYSLIB =	-lfftw -lmpich -lpthread
+SYSLIB =	
 ARCHIVE =	ar
 ARFLAGS =	-rc
 SIZE =		size

examples/COUPLE/lammps_spparks/README

@@ -1,44 +1,67 @@
-IMPORTANT NOTE: This example has not been updated since 2013,
-so it is not likely to work anymore out of the box.  There have
-been changes to LAMMPS and its library interface that would need
-to be applied. Please see the manual for the documentation of
-the library interface.
-
 This directory has an application that models grain growth in the
 presence of strain.
 
-The grain growth is simulated by a Potts model in a kinetic Monte
+The grain growth is simulated by a Potts model in the kinetic Monte
-Carlo code SPPARKS.  Clusters of like spins on a lattice represent
+Carlo code SPPARKS -- https://spparks.github.io
-grains.  The Hamiltonian for the energy due of a collection of spins
-includes a strain term and is described on this page in the SPPARKS
-documentation:
 
-http://spparks.sandia.gov/doc/app_potts_strain.html.
+Clusters of like spins on a lattice represent grains.  The Hamiltonian
+for the energy due of a collection of spins includes a strain term and
+is described on this page in the SPPARKS documentation:
 
-The strain is computed by the molecular dynamics code LAMMPS as a
+https://spparks.github.io/doc/app_potts_strain.html
-particle displacement where pairs of atoms across a grain boundary are
+
-of different types and thus push off from each other due to a
+The strain is computed by the LAMMPS molecular dynamics code --
-Lennard-Jones sigma between particles of different types that is
+https://www.lammps.org -- as a particle displacement where pairs of
-larger than the sigma between particles of the same type (interior to
+atoms across a grain boundary are of different types and thus push off
-grains).
+from each other due to a Lennard-Jones sigma between particles of
+different types that is larger than the sigma between particles of the
+same type (interior to grains).
 
 lmpspk.cpp          main program
-                    it links LAMMPS and SPPARKS as libraries
+                    it links to LAMMPS and SPPARKS as libraries
 in.spparks          SPPARKS input script, without the run command
 lmppath.h           contains path to LAMMPS home directory
 spkpath.h           contains path to SPPARKS home directory
 
-After editing the Makefile, lmppath.h, and spkpath.h to make them
+-----------------------------------
-suitable for your box, type:
 
-make -f Makefile.g++
+(1) To build and run this coupled application, you must have SPPARKS
+built on your system.  It's WWW site is https://spparks.github.io and
+it can be downloaded as a tarball or cloned as a local Git repo.
 
-and you should get the lmpspk executable.
+To build SPPARKS, do the following:
 
-NOTE: To build and run this coupled application, you must of course,
+% cd spparks/src
-have SPPARKS built on your system.  It's WWW site is
+% make mpi
-http://www.sandia.gov/~sjplimp/spparks.html.  It is an open-source
+% make mode=lib mpi      # build SPPARKS as a library
-code, written by two of the LAMMPS authors.
+
+-----------------------------------
+
+(2) You must also build the coupling library in
+lammps/examples/COUPLE/library.
+
+To build the coupling library, do the following:
+
+% cd lammps/examples/COUPLE/library
+% make -f Makefile.mpi
+
+-----------------------------------
+
+(3) Edit the Makefile.mpi, lmppath.h, and spkpath.h files in this
+directory to make them suitable for your box.  Each of the 3 files
+has a comment telling you what to do.
+
+-----------------------------------
+
+(4) Build the coupled lmpspk application in this directory.
+
+% make -f Makefile.mpi
+
+This should give you a lmpspk executable.
+
+-----------------------------------
+
+(5) Run the test simulation
 
 You can run lmpspk in serial or parallel as:
 
@@ -52,7 +75,7 @@ Ndelta = time to run MC in each iteration
 Sfactor = multiplier on strain effect
 in.spparks = SPPARKS input script
 
-The log files are for this run:
+The log files included in this directory are for this run:
 
 % lmpspk 20 10.0 1 in.spparks
 
@@ -70,11 +93,15 @@ The driver code launches both SPPARKS and LAMMPS in parallel and they
 both decompose their spatial domains in the same manner.  The datums
 in SPPARKS (lattice sites) are the same as the datums in LAMMPS
 (coarse-grained particles).  If this were not the case, more
-sophisticated inter-code communication could be performed.
+sophisticated inter-code communication could be performed.  Note that
+the in.lammps and data.lammps files are not inputs; they are generated
+by the lmpspk driver.
 
-You can look at the log files in the directory to see sample LAMMPS
+You can look at the log files in the directory to see LAMMPS and
-and SPPARKS output for this simulation.  Dump files produced by the
+SPPARKS output for this simulation run on 1 and 4 processors.  Dump
-run are stored as dump.mc and dump.md.  The image*.png files show
+files produced by the run are named dump.mc and dump.md.  The image
-snapshots from both the LAMMPS and SPPARKS output.  Note that the
+PPM files show snapshots from the SPPARKS and LAMMPS output.  Compare
-in.lammps and data.lammps files are not inputs; they are generated by
+the image_spparks.0019.ppm and image_lammps.0190.ppm file.  They were
-the lmpspk driver.
+written at the same point in the simulation by both codes.  The color
+maps for the 2 codes are not the same, but the morphology of the
+grains is.

examples/COUPLE/lammps_spparks/in.lammps

@@ -111,4 +111,6 @@ pair_coeff 100 100 1.0 1.0
 compute da all displace/atom
 
 dump 1 all atom 10 dump.md
+dump 2 all image 10 image_lammps.*.ppm type type zoom 1.6
+dump_modify 2 pad 4 acolor * red/green/blue/aqua/magenta/yellow
 thermo 1

examples/COUPLE/lammps_spparks/in.spparks

@@ -20,4 +20,8 @@ diag_style       energy
 temperature	 1.0
 
 stats            10.0
-dump             1 10.0 dump.mc
+dump             1 text 10.0 dump.mc id site x y
+
+dump 		 2 image 1000 image_spparks.*.ppm site site view 0 0 box no 0.1 &
+                 crange 1 100 drange 1 1 shape cube zoom 1.5 size 512 512
+dump_modify 	 2 pad 4

examples/COUPLE/lammps_spparks/lmppath.h

@@ -1 +1,3 @@
-#define LMPPATH /home/sjplimp/lammps 
+// path to your LAMMPS home directory
+
+#define LMPPATH /home/sjplimp/lammps/git

examples/COUPLE/lammps_spparks/lmpspk.cpp

@@ -14,8 +14,8 @@
 
 #include "lammps_data_write.h"
 #include "many2many.h"
-#include "memory.h"
+#include "memorylib.h"
-#include "error.h"
+#include "errorlib.h"
 
 #define QUOTE_(x) #x
 #define QUOTE(x) QUOTE_(x)
@@ -51,8 +51,8 @@ int main(int narg, char **arg)
   MPI_Comm_rank(comm,&me);
   MPI_Comm_size(comm,&nprocs);
 
-  Memory *memory = new Memory(comm);
+  MemoryLib *memory = new MemoryLib(comm);
-  Error *error = new Error(comm);
+  ErrorLib *error = new ErrorLib(comm);
 
   // command-line args
 
@@ -83,28 +83,28 @@ int main(int narg, char **arg)
   double **xyz;
   double *strain;
 
-  dimension = *((int *) spparks_extract(spk,"dimension"));
+  dimension = *((int *) spparks_extract(spk,(char *) "dimension"));
-  nglobal = *((int *) spparks_extract(spk,"nglobal"));
+  nglobal = *((int *) spparks_extract(spk,(char *) "nglobal"));
-  nlocal_spparks = *((int *) spparks_extract(spk,"nlocal"));
+  nlocal_spparks = *((int *) spparks_extract(spk,(char *) "nlocal"));
 
-  boxxlo = *((double *) spparks_extract(spk,"boxxlo"));
+  boxxlo = *((double *) spparks_extract(spk,(char *) "boxxlo"));
-  boxxhi = *((double *) spparks_extract(spk,"boxxhi"));
+  boxxhi = *((double *) spparks_extract(spk,(char *) "boxxhi"));
-  boxylo = *((double *) spparks_extract(spk,"boxylo"));
+  boxylo = *((double *) spparks_extract(spk,(char *) "boxylo"));
-  boxyhi = *((double *) spparks_extract(spk,"boxyhi"));
+  boxyhi = *((double *) spparks_extract(spk,(char *) "boxyhi"));
   if (dimension == 3) {
-    boxzlo = *((double *) spparks_extract(spk,"boxzlo"));
+    boxzlo = *((double *) spparks_extract(spk,(char *) "boxzlo"));
-    boxzhi = *((double *) spparks_extract(spk,"boxzhi"));
+    boxzhi = *((double *) spparks_extract(spk,(char *) "boxzhi"));
   } else {
     boxzlo = -0.5;
     boxzhi = 0.5;
   }
 
-  id_spparks = (int *) spparks_extract(spk,"id");
+  id_spparks = (int *) spparks_extract(spk,(char *) "id");
-  spins = (int *) spparks_extract(spk,"site");
+  spins = (int *) spparks_extract(spk,(char *) "site");
-  xyz = (double **) spparks_extract(spk,"xyz");
+  xyz = (double **) spparks_extract(spk,(char *) "xyz");
 
-  nspins = *((int *) spparks_extract(spk,"nspins"));
+  nspins = *((int *) spparks_extract(spk,(char *) "nspins"));
-  strain = (double *) spparks_extract(spk,"strain");
+  strain = (double *) spparks_extract(spk,(char *) "strain");
 
   // write a LAMMPS input script using SPPARKS params
 
@@ -114,7 +114,7 @@ int main(int narg, char **arg)
 
     fprintf(fp,"units lj\n");
     sprintf(str,"dimension %d\n",dimension);
-    fprintf(fp,str);
+    fprintf(fp,"%s",str);
     fprintf(fp,"atom_style atomic\n\n");
     
     fprintf(fp,"read_data data.lammps\n");
@@ -124,12 +124,14 @@ int main(int narg, char **arg)
     fprintf(fp,"pair_coeff * * 1.0 1.2\n");
     for (i = 0; i < nspins; i++) {
       sprintf(str,"pair_coeff %d %d 1.0 1.0\n",i+1,i+1);
-      fprintf(fp,str);
+      fprintf(fp,"%s",str);
     }
     fprintf(fp,"\n");
 
     fprintf(fp,"compute da all displace/atom\n\n");
     fprintf(fp,"dump 1 all atom 10 dump.md\n");
+    fprintf(fp,"dump 2 all image 10 image_lammps.*.ppm type type zoom 1.6\n");
+    fprintf(fp,"dump_modify 2 pad 4 acolor * red/green/blue/aqua/magenta/yellow\n");
     fprintf(fp,"thermo 1\n");
 
     fclose(fp);
@@ -138,12 +140,12 @@ int main(int narg, char **arg)
   // write a LAMMPS data file using SPPARKS data
 
   LAMMPSDataWrite *lwd = new LAMMPSDataWrite(MPI_COMM_WORLD);
-  lwd->file("data.lammps");
+  lwd->file((char *) "data.lammps");
-  lwd->header("%d atoms",nglobal);
+  lwd->header((char *) "%d atoms",nglobal);
-  lwd->header("%d atom types",nspins);
+  lwd->header((char *) "%d atom types",nspins);
-  lwd->header("%g %g xlo xhi",boxxlo,boxxhi);
+  lwd->header((char *) "%g %g xlo xhi",boxxlo,boxxhi);
-  lwd->header("%g %g ylo yhi",boxylo,boxyhi);
+  lwd->header((char *) "%g %g ylo yhi",boxylo,boxyhi);
-  lwd->header("%g %g zlo zhi",boxzlo,boxzhi);
+  lwd->header((char *) "%g %g zlo zhi",boxzlo,boxzhi);
   lwd->atoms(nlocal_spparks);
   lwd->atoms(id_spparks);
   lwd->atoms(spins);

examples/COUPLE/lammps_spparks/log.spparks.1

@@ -1,4 +1,4 @@
-SPPARKS (26 Aug 2010)
+SPPARKS (19 Sept 2022)
 # SPPARKS input for coupling MD/MC
 
 seed		 56789
@@ -28,244 +28,246 @@ diag_style       energy
 temperature	 1.0
 
 stats            10.0
-dump             1 10.0 dump.mc
+dump             1 text 10.0 dump.mc id site x y
 run 10Setting up run ...
+Running with 32-bit site IDs
+Memory usage per processor = 2.375 Mbytes
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
          0          0          0          0          0      19766
-        10      17929          0          0     0.0776       5324
+        10      18978          0         13     0.0259       5500
-Loop time of 0.077626 on 1 procs
+Loop time of 0.0258905 on 1 procs
 
-Solve time (%) = 0.0070138 (9.03537)
+Solve time (%) = 0.00155363 (6.00079)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00146031 (1.88122)
+Comm  time (%) = 0.000642316 (2.4809)
-Outpt time (%) = 0.00415015 (5.34634)
+Outpt time (%) = 0.000680321 (2.62769)
-App   time (%) = 0.0614648 (79.1807)
+App   time (%) = 0.0226682 (87.5542)
-Other time (%) = 0.00353694 (4.55639)
+Other time (%) = 0.000346003 (1.33641)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        10      17929          0          0          0       5324
+        10      18978          0         13          0       5500
-        20      24582          0          0     0.0279       4750
+        20      25374          0         18    0.00709       4552
-Loop time of 0.027904 on 1 procs
+Loop time of 0.00708869 on 1 procs
 
-Solve time (%) = 0.00271416 (9.72676)
+Solve time (%) = 0.000496193 (6.99978)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000461817 (1.65502)
+Comm  time (%) = 0.000158039 (2.22945)
-Outpt time (%) = 0.0042181 (15.1165)
+Outpt time (%) = 0.0006739 (9.50669)
-App   time (%) = 0.0191288 (68.5521)
+App   time (%) = 0.00564639 (79.6535)
-Other time (%) = 0.00138116 (4.94967)
+Other time (%) = 0.000114167 (1.61055)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        20      24582          0          0          0       4750
+        20      25374          0         18          0       4552
-        30      30109          0          0     0.0234       4264
+        30      30752          0         23    0.00575       4096
-Loop time of 0.023375 on 1 procs
+Loop time of 0.00575649 on 1 procs
 
-Solve time (%) = 0.00216675 (9.2695)
+Solve time (%) = 0.000415252 (7.21363)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000342846 (1.46672)
+Comm  time (%) = 0.00013092 (2.2743)
-Outpt time (%) = 0.00416183 (17.8046)
+Outpt time (%) = 0.000662723 (11.5126)
-App   time (%) = 0.015563 (66.5796)
+App   time (%) = 0.00445117 (77.3244)
-Other time (%) = 0.00114059 (4.87954)
+Other time (%) = 9.6422e-05 (1.67501)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        30      30109          0          0          0       4264
+        30      30752          0         23          0       4096
-        40      35032          0          0     0.0208       3880
+        40      35529          0         27    0.00589       3596
-Loop time of 0.020786 on 1 procs
+Loop time of 0.00589801 on 1 procs
 
-Solve time (%) = 0.0019896 (9.57182)
+Solve time (%) = 0.000424563 (7.19841)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000316858 (1.52438)
+Comm  time (%) = 0.000114131 (1.93508)
-Outpt time (%) = 0.00413609 (19.8984)
+Outpt time (%) = 0.000763593 (12.9466)
-App   time (%) = 0.0132952 (63.962)
+App   time (%) = 0.0044969 (76.2443)
-Other time (%) = 0.00104833 (5.04341)
+Other time (%) = 9.8828e-05 (1.67562)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        40      35032          0          0          0       3880
+        40      35529          0         27          0       3596
-        50      39543          0          0     0.0193       3784
+        50      39736          0         31    0.00444       3298
-Loop time of 0.0193491 on 1 procs
+Loop time of 0.00444854 on 1 procs
 
-Solve time (%) = 0.00185919 (9.60865)
+Solve time (%) = 0.000323247 (7.26637)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000333071 (1.72138)
+Comm  time (%) = 9.6777e-05 (2.17548)
-Outpt time (%) = 0.00412297 (21.3083)
+Outpt time (%) = 0.000637529 (14.3312)
-App   time (%) = 0.0120728 (62.3946)
+App   time (%) = 0.00331502 (74.5193)
-Other time (%) = 0.000961065 (4.96698)
+Other time (%) = 7.5967e-05 (1.70769)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        50      39543          0          0          0       3784
+        50      39736          0         31          0       3298
-        60      43899          0          0     0.0187       3706
+        60      43567          0         35    0.00507       3296
-Loop time of 0.018713 on 1 procs
+Loop time of 0.0050729 on 1 procs
 
-Solve time (%) = 0.00176001 (9.40526)
+Solve time (%) = 0.000354098 (6.98019)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000314474 (1.68051)
+Comm  time (%) = 0.000114818 (2.26336)
-Outpt time (%) = 0.00413895 (22.118)
+Outpt time (%) = 0.000893366 (17.6106)
-App   time (%) = 0.0116153 (62.0706)
+App   time (%) = 0.00362051 (71.3697)
-Other time (%) = 0.000884295 (4.72556)
+Other time (%) = 9.0105e-05 (1.7762)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        60      43899          0          0          0       3706
+        60      43567          0         35          0       3296
-        70      48028          0          0     0.0179       3392
+        70      47305          0         39    0.00417       3174
-Loop time of 0.0178769 on 1 procs
+Loop time of 0.00417405 on 1 procs
 
-Solve time (%) = 0.00174618 (9.76781)
+Solve time (%) = 0.00030627 (7.33747)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000296593 (1.65909)
+Comm  time (%) = 9.1156e-05 (2.18387)
-Outpt time (%) = 0.00414801 (23.2032)
+Outpt time (%) = 0.000689193 (16.5114)
-App   time (%) = 0.0108221 (60.5367)
+App   time (%) = 0.00301511 (72.2347)
-Other time (%) = 0.000864029 (4.83322)
+Other time (%) = 7.232e-05 (1.73261)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        70      48028          0          0          0       3392
+        70      47305          0         39          0       3174
-        80      51900          0          0      0.017       3208
+        80      51214          0         43    0.00437       3252
-Loop time of 0.0169971 on 1 procs
+Loop time of 0.00437516 on 1 procs
 
-Solve time (%) = 0.00157022 (9.23819)
+Solve time (%) = 0.000332427 (7.59805)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000290394 (1.70849)
+Comm  time (%) = 9.1593e-05 (2.09348)
-Outpt time (%) = 0.00416803 (24.522)
+Outpt time (%) = 0.00064481 (14.738)
-App   time (%) = 0.0101995 (60.0076)
+App   time (%) = 0.00323051 (73.8375)
-Other time (%) = 0.0007689 (4.52371)
+Other time (%) = 7.5822e-05 (1.73301)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        80      51900          0          0          0       3208
+        80      51214          0         43          0       3252
-        90      55450          0          0     0.0159       3162
+        90      54863          0         47    0.00417       3016
-Loop time of 0.0158761 on 1 procs
+Loop time of 0.00417621 on 1 procs
 
-Solve time (%) = 0.0014894 (9.38143)
+Solve time (%) = 0.000285188 (6.82887)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000301123 (1.89671)
+Comm  time (%) = 9.0115e-05 (2.15782)
-Outpt time (%) = 0.00413799 (26.0644)
+Outpt time (%) = 0.000719767 (17.2349)
-App   time (%) = 0.00924802 (58.2514)
+App   time (%) = 0.00301373 (72.1642)
-Other time (%) = 0.00069952 (4.40613)
+Other time (%) = 6.7413e-05 (1.61421)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        90      55450          0          0          0       3162
+        90      54863          0         47          0       3016
-       100      59009          0          0     0.0158       3038
+       100      58060          0         51    0.00369       2766
-Loop time of 0.0158172 on 1 procs
+Loop time of 0.00369187 on 1 procs
 
-Solve time (%) = 0.00142503 (9.00938)
+Solve time (%) = 0.000253511 (6.86674)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000296831 (1.87664)
+Comm  time (%) = 8.878e-05 (2.40475)
-Outpt time (%) = 0.00412178 (26.0589)
+Outpt time (%) = 0.000686238 (18.5878)
-App   time (%) = 0.00923729 (58.4004)
+App   time (%) = 0.00260318 (70.5111)
-Other time (%) = 0.000736237 (4.65467)
+Other time (%) = 6.0163e-05 (1.62961)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       100      59009          0          0          0       3038
+       100      58060          0         51          0       2766
-       110      62454          0          0     0.0155       3066
+       110      61110          0         55    0.00349       2840
-Loop time of 0.015537 on 1 procs
+Loop time of 0.00349695 on 1 procs
 
-Solve time (%) = 0.00135612 (8.72834)
+Solve time (%) = 0.000239587 (6.85131)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000293732 (1.89053)
+Comm  time (%) = 8.1517e-05 (2.33109)
-Outpt time (%) = 0.00415182 (26.7221)
+Outpt time (%) = 0.000719507 (20.5753)
-App   time (%) = 0.00904965 (58.2457)
+App   time (%) = 0.0023994 (68.614)
-Other time (%) = 0.000685692 (4.41328)
+Other time (%) = 5.6943e-05 (1.62836)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       110      62454          0          0          0       3066
+       110      61110          0         55          0       2840
-       120      65856          0          0     0.0152       2898
+       120      64087          0         59    0.00325       2714
-Loop time of 0.0152211 on 1 procs
+Loop time of 0.00324861 on 1 procs
 
-Solve time (%) = 0.00139046 (9.13505)
+Solve time (%) = 0.000225271 (6.93437)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000291109 (1.91253)
+Comm  time (%) = 8.3445e-05 (2.56863)
-Outpt time (%) = 0.0041492 (27.2595)
+Outpt time (%) = 0.000647543 (19.9329)
-App   time (%) = 0.00871038 (57.2257)
+App   time (%) = 0.00223748 (68.8748)
-Other time (%) = 0.00067997 (4.46728)
+Other time (%) = 5.4877e-05 (1.68924)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       120      65856          0          0          0       2898
+       120      64087          0         59          0       2714
-       130      68856          0          0     0.0137       2798
+       130      67004          0         63    0.00333       2664
-Loop time of 0.0137191 on 1 procs
+Loop time of 0.00333198 on 1 procs
 
-Solve time (%) = 0.00130701 (9.52695)
+Solve time (%) = 0.00022963 (6.89169)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000296831 (2.16364)
+Comm  time (%) = 9.0368e-05 (2.71214)
-Outpt time (%) = 0.00412989 (30.1032)
+Outpt time (%) = 0.000650383 (19.5194)
-App   time (%) = 0.00742817 (54.1448)
+App   time (%) = 0.00230627 (69.2163)
-Other time (%) = 0.000557184 (4.06138)
+Other time (%) = 5.5328e-05 (1.66051)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       130      68856          0          0          0       2798
+       130      67004          0         63          0       2664
-       140      71967          0          0     0.0141       2700
+       140      69933          0         67    0.00324       2680
-Loop time of 0.0141542 on 1 procs
+Loop time of 0.00324401 on 1 procs
 
-Solve time (%) = 0.00132799 (9.38232)
+Solve time (%) = 0.000227399 (7.00982)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000284195 (2.00785)
+Comm  time (%) = 8.818e-05 (2.71824)
-Outpt time (%) = 0.00414681 (29.2974)
+Outpt time (%) = 0.000638812 (19.6921)
-App   time (%) = 0.00777125 (54.9042)
+App   time (%) = 0.00223398 (68.8649)
-Other time (%) = 0.000623941 (4.40817)
+Other time (%) = 5.5635e-05 (1.71501)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       140      71967          0          0          0       2700
+       140      69933          0         67          0       2680
-       150      74773          0          0     0.0132       2644
+       150      72830          0         71    0.00314       2664
-Loop time of 0.0131881 on 1 procs
+Loop time of 0.0031476 on 1 procs
 
-Solve time (%) = 0.00111961 (8.48956)
+Solve time (%) = 0.000213509 (6.78324)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000277758 (2.10612)
+Comm  time (%) = 8.6263e-05 (2.7406)
-Outpt time (%) = 0.00413394 (31.3459)
+Outpt time (%) = 0.000676177 (21.4823)
-App   time (%) = 0.00711513 (53.951)
+App   time (%) = 0.00211915 (67.326)
-Other time (%) = 0.000541687 (4.10738)
+Other time (%) = 5.2495e-05 (1.66778)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       150      74773          0          0          0       2644
+       150      72830          0         71          0       2664
-       160      77662          0          0     0.0134       2616
+       160      75877          0         75    0.00386       2640
-Loop time of 0.0133891 on 1 procs
+Loop time of 0.00386614 on 1 procs
 
-Solve time (%) = 0.00116301 (8.68621)
+Solve time (%) = 0.000262699 (6.79487)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00027895 (2.08341)
+Comm  time (%) = 0.000115859 (2.99676)
-Outpt time (%) = 0.00415397 (31.025)
+Outpt time (%) = 0.000745615 (19.2858)
-App   time (%) = 0.00725079 (54.1544)
+App   time (%) = 0.00267785 (69.2643)
-Other time (%) = 0.000542402 (4.05107)
+Other time (%) = 6.4111e-05 (1.65827)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       160      77662          0          0          0       2616
+       160      75877          0         75          0       2640
-       170      80475          0          0     0.0131       2538
+       170      78733          0         79    0.00555       2486
-Loop time of 0.0130939 on 1 procs
+Loop time of 0.0055484 on 1 procs
 
-Solve time (%) = 0.00108457 (8.28296)
+Solve time (%) = 0.000407211 (7.33925)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000279665 (2.13583)
+Comm  time (%) = 0.000168943 (3.04489)
-Outpt time (%) = 0.00412798 (31.5259)
+Outpt time (%) = 0.000823976 (14.8507)
-App   time (%) = 0.00700951 (53.5324)
+App   time (%) = 0.00404893 (72.9746)
-Other time (%) = 0.000592232 (4.52294)
+Other time (%) = 9.9346e-05 (1.79053)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       170      80475          0          0          0       2538
+       170      78733          0         79          0       2486
-       180      83407          0          0     0.0136       2660
+       180      81400          0         83    0.00291       2396
-Loop time of 0.0136199 on 1 procs
+Loop time of 0.00291697 on 1 procs
 
-Solve time (%) = 0.00117278 (8.61079)
+Solve time (%) = 0.000197105 (6.75718)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000262737 (1.92907)
+Comm  time (%) = 8.6733e-05 (2.97339)
-Outpt time (%) = 0.00413108 (30.3312)
+Outpt time (%) = 0.000641861 (22.0044)
-App   time (%) = 0.0074532 (54.7229)
+App   time (%) = 0.00194335 (66.6221)
-Other time (%) = 0.0006001 (4.40605)
+Other time (%) = 4.7923e-05 (1.6429)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       180      83407          0          0          0       2660
+       180      81400          0         83          0       2396
-       190      86407          0          0     0.0138       2656
+       190      84097          0         86    0.00291       2418
-Loop time of 0.013859 on 1 procs
+Loop time of 0.00290961 on 1 procs
 
-Solve time (%) = 0.00119066 (8.59124)
+Solve time (%) = 0.000198685 (6.82859)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000247717 (1.7874)
+Comm  time (%) = 6.5496e-05 (2.25103)
-Outpt time (%) = 0.00414801 (29.93)
+Outpt time (%) = 0.000671627 (23.0831)
-App   time (%) = 0.00767326 (55.3665)
+App   time (%) = 0.00192582 (66.1883)
-Other time (%) = 0.000599384 (4.32486)
+Other time (%) = 4.7978e-05 (1.64895)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       190      86407          0          0          0       2656
+       190      84097          0         86          0       2418
-       200      88961          0          0     0.0124       2374
+       200      86656          0         90    0.00332       2442
-Loop time of 0.0124531 on 1 procs
+Loop time of 0.00332468 on 1 procs
 
-Solve time (%) = 0.00107932 (8.6671)
+Solve time (%) = 0.000220838 (6.64238)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000233412 (1.87433)
+Comm  time (%) = 9.3912e-05 (2.82469)
-Outpt time (%) = 0.00414777 (33.3072)
+Outpt time (%) = 0.000744786 (22.4017)
-App   time (%) = 0.00648117 (52.0447)
+App   time (%) = 0.00221113 (66.5064)
-Other time (%) = 0.000511408 (4.10668)
+Other time (%) = 5.402e-05 (1.62482)

examples/COUPLE/lammps_spparks/log.spparks.4

@@ -1,4 +1,4 @@
-SPPARKS (26 Aug 2010)
+SPPARKS (19 Sept 2022)
 # SPPARKS input for coupling MD/MC
 
 seed		 56789
@@ -28,244 +28,246 @@ diag_style       energy
 temperature	 1.0
 
 stats            10.0
-dump             1 10.0 dump.mc
+dump             1 text 10.0 dump.mc id site x y
 run 10Setting up run ...
+Running with 32-bit site IDs
+Memory usage per processor = 2.375 Mbytes
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
          0          0          0          0          0      19766
-        10      18695          0          0      0.024       5696
+        10      18709          0         14    0.00995       5410
-Loop time of 0.0240365 on 4 procs
+Loop time of 0.00996147 on 4 procs
 
-Solve time (%) = 0.0017997 (7.48737)
+Solve time (%) = 0.000401817 (4.03371)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00263286 (10.9536)
+Comm  time (%) = 0.00184758 (18.5473)
-Outpt time (%) = 0.00416493 (17.3275)
+Outpt time (%) = 0.000835493 (8.38724)
-App   time (%) = 0.0137114 (57.044)
+App   time (%) = 0.00643178 (64.5665)
-Other time (%) = 0.00172764 (7.18756)
+Other time (%) = 0.000444804 (4.46524)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        10      18695          0          0          0       5696
+        10      18709          0         14          0       5410
-        20      25730          0          0     0.0114       4806
+        20      25405          0         20    0.00348       4414
-Loop time of 0.0113776 on 4 procs
+Loop time of 0.00348928 on 4 procs
 
-Solve time (%) = 0.000647247 (5.68877)
+Solve time (%) = 0.000145149 (4.15985)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.0013088 (11.5033)
+Comm  time (%) = 0.000562263 (16.114)
-Outpt time (%) = 0.00417346 (36.6812)
+Outpt time (%) = 0.0007944 (22.7669)
-App   time (%) = 0.0045594 (40.0733)
+App   time (%) = 0.00176801 (50.6697)
-Other time (%) = 0.000688732 (6.05338)
+Other time (%) = 0.000219463 (6.28963)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        20      25730          0          0          0       4806
+        20      25405          0         20          0       4414
-        30      31377          0          0    0.00985       4308
+        30      30724          0         25    0.00314       4092
-Loop time of 0.00987101 on 4 procs
+Loop time of 0.00314216 on 4 procs
 
-Solve time (%) = 0.000525832 (5.32704)
+Solve time (%) = 0.000123228 (3.92176)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.0012235 (12.3949)
+Comm  time (%) = 0.000561445 (17.8681)
-Outpt time (%) = 0.00415748 (42.1181)
+Outpt time (%) = 0.00079681 (25.3586)
-App   time (%) = 0.00343758 (34.825)
+App   time (%) = 0.00146373 (46.5835)
-Other time (%) = 0.000526607 (5.33489)
+Other time (%) = 0.000196952 (6.26804)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        30      31377          0          0          0       4308
+        30      30724          0         25          0       4092
-        40      36311          0          0     0.0092       3840
+        40      35289          0         30    0.00256       3496
-Loop time of 0.00922179 on 4 procs
+Loop time of 0.0025659 on 4 procs
 
-Solve time (%) = 0.000474155 (5.14168)
+Solve time (%) = 9.47535e-05 (3.6928)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00114667 (12.4344)
+Comm  time (%) = 0.000508415 (19.8143)
-Outpt time (%) = 0.00414455 (44.943)
+Outpt time (%) = 0.000788757 (30.74)
-App   time (%) = 0.00293165 (31.7905)
+App   time (%) = 0.00106383 (41.4604)
-Other time (%) = 0.000524759 (5.69043)
+Other time (%) = 0.000110143 (4.29259)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        40      36311          0          0          0       3840
+        40      35289          0         30          0       3496
-        50      40886          0          0    0.00891       3534
+        50      39511          0         35    0.00252       3294
-Loop time of 0.0089252 on 4 procs
+Loop time of 0.00252512 on 4 procs
 
-Solve time (%) = 0.000433862 (4.86109)
+Solve time (%) = 8.7092e-05 (3.44903)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00113171 (12.68)
+Comm  time (%) = 0.000631729 (25.0178)
-Outpt time (%) = 0.00413698 (46.3517)
+Outpt time (%) = 0.000780138 (30.8952)
-App   time (%) = 0.00268257 (30.0561)
+App   time (%) = 0.000963016 (38.1375)
-Other time (%) = 0.000540078 (6.05116)
+Other time (%) = 6.31405e-05 (2.5005)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        50      40886          0          0          0       3534
+        50      39511          0         35          0       3294
-        60      44888          0          0    0.00831       3306
+        60      43241          0         40    0.00254       3158
-Loop time of 0.00833625 on 4 procs
+Loop time of 0.00254794 on 4 procs
 
-Solve time (%) = 0.000383437 (4.59963)
+Solve time (%) = 8.5528e-05 (3.35675)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00106108 (12.7285)
+Comm  time (%) = 0.000598337 (23.4831)
-Outpt time (%) = 0.00413227 (49.5699)
+Outpt time (%) = 0.000777931 (30.5317)
-App   time (%) = 0.00232393 (27.8774)
+App   time (%) = 0.000940118 (36.8971)
-Other time (%) = 0.000435531 (5.22455)
+Other time (%) = 0.00014603 (5.73128)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        60      44888          0          0          0       3306
+        60      43241          0         40          0       3158
-        70      48583          0          0    0.00806       3078
+        70      46797          0         44    0.00248       3060
-Loop time of 0.0080772 on 4 procs
+Loop time of 0.00248266 on 4 procs
 
-Solve time (%) = 0.000353277 (4.37375)
+Solve time (%) = 8.14515e-05 (3.28081)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00102895 (12.739)
+Comm  time (%) = 0.000482648 (19.4407)
-Outpt time (%) = 0.0041061 (50.8357)
+Outpt time (%) = 0.000991271 (39.9277)
-App   time (%) = 0.00213838 (26.4742)
+App   time (%) = 0.00085854 (34.5814)
-Other time (%) = 0.000450492 (5.57732)
+Other time (%) = 6.87532e-05 (2.76933)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        70      48583          0          0          0       3078
+        70      46797          0         44          0       3060
-        80      52044          0          0    0.00786       2998
+        80      50183          0         48     0.0024       3102
-Loop time of 0.00788343 on 4 procs
+Loop time of 0.00240397 on 4 procs
 
-Solve time (%) = 0.000333607 (4.23175)
+Solve time (%) = 8.22802e-05 (3.42268)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00101435 (12.8669)
+Comm  time (%) = 0.000494873 (20.5856)
-Outpt time (%) = 0.00420028 (53.2799)
+Outpt time (%) = 0.00085299 (35.4825)
-App   time (%) = 0.00198931 (25.234)
+App   time (%) = 0.000883469 (36.7504)
-Other time (%) = 0.000345886 (4.3875)
+Other time (%) = 9.03613e-05 (3.75883)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        80      52044          0          0          0       2998
+        80      50183          0         48          0       3102
-        90      55352          0          0     0.0083       3026
+        90      53732          0         52    0.00272       3028
-Loop time of 0.00831437 on 4 procs
+Loop time of 0.00272017 on 4 procs
 
-Solve time (%) = 0.00031358 (3.77154)
+Solve time (%) = 9.94713e-05 (3.6568)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00111783 (13.4445)
+Comm  time (%) = 0.000613542 (22.5553)
-Outpt time (%) = 0.00467652 (56.2462)
+Outpt time (%) = 0.000800183 (29.4166)
-App   time (%) = 0.00188529 (22.6751)
+App   time (%) = 0.00108281 (39.8067)
-Other time (%) = 0.00032115 (3.86259)
+Other time (%) = 0.000124164 (4.56456)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-        90      55352          0          0          0       3026
+        90      53732          0         52          0       3028
-       100      58494          0          0    0.00733       2742
+       100      57112          0         56     0.0023       2942
-Loop time of 0.00735307 on 4 procs
+Loop time of 0.00230787 on 4 procs
 
-Solve time (%) = 0.000297189 (4.0417)
+Solve time (%) = 7.58975e-05 (3.28864)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000801027 (10.8938)
+Comm  time (%) = 0.000502726 (21.7831)
-Outpt time (%) = 0.00418043 (56.8529)
+Outpt time (%) = 0.000796114 (34.4956)
-App   time (%) = 0.00179577 (24.422)
+App   time (%) = 0.000828819 (35.9127)
-Other time (%) = 0.000278652 (3.7896)
+Other time (%) = 0.000104316 (4.51999)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       100      58494          0          0          0       2742
+       100      57112          0         56          0       2942
-       110      61498          0          0    0.00732       2636
+       110      60445          0         60    0.00192       2850
-Loop time of 0.00733691 on 4 procs
+Loop time of 0.00192261 on 4 procs
 
-Solve time (%) = 0.000282168 (3.84587)
+Solve time (%) = 6.89883e-05 (3.58826)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000877678 (11.9625)
+Comm  time (%) = 0.000257782 (13.4079)
-Outpt time (%) = 0.00414526 (56.4987)
+Outpt time (%) = 0.000791242 (41.1545)
-App   time (%) = 0.00174332 (23.7609)
+App   time (%) = 0.000735212 (38.2403)
-Other time (%) = 0.000288486 (3.93199)
+Other time (%) = 6.9388e-05 (3.60905)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       110      61498          0          0          0       2636
+       110      60445          0         60          0       2850
-       120      64343          0          0    0.00719       2518
+       120      63603          0         64    0.00193       2866
-Loop time of 0.00721735 on 4 procs
+Loop time of 0.00193198 on 4 procs
 
-Solve time (%) = 0.000270605 (3.74937)
+Solve time (%) = 6.44032e-05 (3.33354)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00078702 (10.9046)
+Comm  time (%) = 0.00027428 (14.1969)
-Outpt time (%) = 0.00416625 (57.7254)
+Outpt time (%) = 0.000812462 (42.0534)
-App   time (%) = 0.00162369 (22.497)
+App   time (%) = 0.000682923 (35.3484)
-Other time (%) = 0.000369787 (5.12359)
+Other time (%) = 9.79088e-05 (5.0678)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       120      64343          0          0          0       2518
+       120      63603          0         64          0       2866
-       130      66901          0          0    0.00709       2480
+       130      66749          0         68     0.0022       2710
-Loop time of 0.00710845 on 4 procs
+Loop time of 0.00220226 on 4 procs
 
-Solve time (%) = 0.000247002 (3.47476)
+Solve time (%) = 8.013e-05 (3.63854)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00100386 (14.1221)
+Comm  time (%) = 0.000362387 (16.4552)
-Outpt time (%) = 0.00416774 (58.6307)
+Outpt time (%) = 0.000819649 (37.2186)
-App   time (%) = 0.00143349 (20.166)
+App   time (%) = 0.000844146 (38.3309)
-Other time (%) = 0.00025636 (3.60641)
+Other time (%) = 9.59462e-05 (4.35672)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       130      66901          0          0          0       2480
+       130      66749          0         68          0       2710
-       140      69617          0          0    0.00723       2462
+       140      69868          0         72    0.00276       2822
-Loop time of 0.00725645 on 4 procs
+Loop time of 0.00276561 on 4 procs
 
-Solve time (%) = 0.000262678 (3.61992)
+Solve time (%) = 8.8444e-05 (3.19799)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000848353 (11.691)
+Comm  time (%) = 0.000566006 (20.4659)
-Outpt time (%) = 0.00418752 (57.7076)
+Outpt time (%) = 0.00100224 (36.2395)
-App   time (%) = 0.00152171 (20.9704)
+App   time (%) = 0.000938724 (33.9427)
-Other time (%) = 0.000436187 (6.01102)
+Other time (%) = 0.000170192 (6.15388)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       140      69617          0          0          0       2462
+       140      69868          0         72          0       2822
-       150      72516          0          0     0.0077       2368
+       150      72809          0         77    0.00203       2530
-Loop time of 0.00771403 on 4 procs
+Loop time of 0.00203296 on 4 procs
 
-Solve time (%) = 0.000279188 (3.61922)
+Solve time (%) = 6.10922e-05 (3.00508)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00115103 (14.9212)
+Comm  time (%) = 0.000430907 (21.196)
-Outpt time (%) = 0.00420797 (54.5495)
+Outpt time (%) = 0.000773949 (38.07)
-App   time (%) = 0.00164241 (21.2911)
+App   time (%) = 0.000649508 (31.9488)
-Other time (%) = 0.000433445 (5.61892)
+Other time (%) = 0.000117508 (5.78011)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       150      72516          0          0          0       2368
+       150      72809          0         77          0       2530
-       160      75201          0          0    0.00745       2384
+       160      75490          0         82    0.00243       2560
-Loop time of 0.00747746 on 4 procs
+Loop time of 0.00243939 on 4 procs
 
-Solve time (%) = 0.00026089 (3.48901)
+Solve time (%) = 7.29237e-05 (2.98943)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00115579 (15.457)
+Comm  time (%) = 0.000533877 (21.8857)
-Outpt time (%) = 0.00416714 (55.7293)
+Outpt time (%) = 0.000900521 (36.9159)
-App   time (%) = 0.0015164 (20.2796)
+App   time (%) = 0.000753532 (30.8902)
-Other time (%) = 0.000377238 (5.045)
+Other time (%) = 0.000178534 (7.31879)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       160      75201          0          0          0       2384
+       160      75490          0         82          0       2560
-       170      77794          0          0    0.00709       2286
+       170      78382          0         86    0.00203       2424
-Loop time of 0.00710869 on 4 procs
+Loop time of 0.00203432 on 4 procs
 
-Solve time (%) = 0.000261724 (3.68175)
+Solve time (%) = 6.05745e-05 (2.97762)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000879705 (12.3751)
+Comm  time (%) = 0.000357404 (17.5687)
-Outpt time (%) = 0.00419676 (59.0371)
+Outpt time (%) = 0.000830967 (40.8473)
-App   time (%) = 0.00145274 (20.4362)
+App   time (%) = 0.000642883 (31.6018)
-Other time (%) = 0.000317752 (4.46992)
+Other time (%) = 0.000142495 (7.00454)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       170      77794          0          0          0       2286
+       170      78382          0         86          0       2424
-       180      80320          0          0    0.00723       2186
+       180      81046          0         90    0.00266       2450
-Loop time of 0.00725418 on 4 procs
+Loop time of 0.00266286 on 4 procs
 
-Solve time (%) = 0.000241041 (3.32279)
+Solve time (%) = 7.05732e-05 (2.65028)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.00100464 (13.8491)
+Comm  time (%) = 0.000638214 (23.9672)
-Outpt time (%) = 0.00413877 (57.0535)
+Outpt time (%) = 0.00102986 (38.6749)
-App   time (%) = 0.00144053 (19.8579)
+App   time (%) = 0.000760398 (28.5557)
-Other time (%) = 0.000429213 (5.91677)
+Other time (%) = 0.000163817 (6.15191)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       180      80320          0          0          0       2186
+       180      81046          0         90          0       2450
-       190      82621          0          0    0.00686       2204
+       190      83562          0         94    0.00216       2402
-Loop time of 0.00687295 on 4 procs
+Loop time of 0.0021675 on 4 procs
 
-Solve time (%) = 0.000222385 (3.23565)
+Solve time (%) = 6.2358e-05 (2.87696)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000860512 (12.5203)
+Comm  time (%) = 0.000536287 (24.7422)
-Outpt time (%) = 0.00418121 (60.8357)
+Outpt time (%) = 0.000802317 (37.0158)
-App   time (%) = 0.00126499 (18.4053)
+App   time (%) = 0.000649124 (29.9481)
-Other time (%) = 0.000343859 (5.00308)
+Other time (%) = 0.000117412 (5.41694)
 run 10Setting up run ...
       Time    Naccept    Nreject    Nsweeps        CPU     Energy
-       190      82621          0          0          0       2204
+       190      83562          0         94          0       2402
-       200      84907          0          0    0.00681       2276
+       200      86036          0         98     0.0021       2306
-Loop time of 0.0068413 on 4 procs
+Loop time of 0.00210625 on 4 procs
 
-Solve time (%) = 0.000233412 (3.4118)
+Solve time (%) = 5.94018e-05 (2.82026)
 Update time (%) = 0 (0)
-Comm  time (%) = 0.000758171 (11.0823)
+Comm  time (%) = 0.000492842 (23.399)
-Outpt time (%) = 0.00421125 (61.5562)
+Outpt time (%) = 0.000817012 (38.7899)
-App   time (%) = 0.00125164 (18.2953)
+App   time (%) = 0.000597335 (28.3601)
-Other time (%) = 0.000386834 (5.65439)
+Other time (%) = 0.00013966 (6.63072)

examples/COUPLE/lammps_spparks/spkpath.h

@@ -1 +1,3 @@
-#define SPKPATH /home/sjplimp/spparks
+// path to your SPPARKS home directory
+
+#define SPKPATH /home/sjplimp/spparks/git

examples/COUPLE/library/README

@@ -6,7 +6,7 @@ SPPARKS applications in 2 sister directories.
 The library dir has a Makefile (which you may need to edit for your
 box).  If you type
 
-g++ -f Makefile.g++
+make -f Makefile.mpi
 
 you should create libcouple.a, which the other coupled applications
 link to.

examples/COUPLE/library/errorlib.cpp

@@ -1,11 +1,11 @@
 #include <mpi.h>
 #include <cstdio>
 #include <cstdlib>
-#include "error.h"
+#include "errorlib.h"
 
 /* ---------------------------------------------------------------------- */
 
-Error::Error(MPI_Comm caller)
+ErrorLib::ErrorLib(MPI_Comm caller)
 {
   comm = caller;
   MPI_Comm_rank(comm,&me);
@@ -15,7 +15,7 @@ Error::Error(MPI_Comm caller)
    called by all procs
 ------------------------------------------------------------------------- */
 
-void Error::all(const char *str)
+void ErrorLib::all(const char *str)
 {
   if (me == 0) printf("ERROR: %s\n",str);
   MPI_Finalize();
@@ -26,7 +26,7 @@ void Error::all(const char *str)
    called by one proc
 ------------------------------------------------------------------------- */
 
-void Error::one(const char *str)
+void ErrorLib::one(const char *str)
 {
   printf("ERROR on proc %d: %s\n",me,str);
   MPI_Abort(comm,1);
@@ -36,7 +36,7 @@ void Error::one(const char *str)
    called by one proc
 ------------------------------------------------------------------------- */
 
-void Error::warning(const char *str)
+void ErrorLib::warning(const char *str)
 {
   printf("WARNING: %s\n",str);
 }

examples/COUPLE/library/errorlib.h

@@ -1,11 +1,11 @@
-#ifndef ERROR_H
+#ifndef ERRORLIB_H
-#define ERROR_H
+#define ERRORLIB_H
 
 #include <mpi.h>
 
-class Error {
+class ErrorLib {
  public:
-  Error(MPI_Comm);
+  ErrorLib(MPI_Comm);
 
   void all(const char *);
   void one(const char *);

examples/COUPLE/library/files.cpp

@@ -29,7 +29,7 @@ void replace(char *file, char *header, int n, char **lines)
 
 /* ---------------------------------------------------------------------- */
 
-char **extract(char *file, char *header, int n, char **lines)
+void extract(char *file, char *header, int n, char **lines)
 {
   FILE *fp = fopen(file,"r");
 

examples/COUPLE/library/files.h

@@ -1,5 +1,5 @@
 #ifndef FILES_H
 #define FILES_H
 void replace(char *, char *, int, char **);
-char **extract(char *, char *, int, char **);
+void extract(char *, char *, int, char **);
 #endif

examples/COUPLE/library/irregular.cpp

@@ -2,8 +2,8 @@
 #include <cstdlib>
 #include <cstring>
 #include "irregular.h"
-#include "memory.h"
+#include "memorylib.h"
-#include "error.h"
+#include "errorlib.h"
 
 #define MAX(A,B) ((A) > (B)) ? (A) : (B)
 
@@ -18,8 +18,8 @@ Irregular::Irregular(MPI_Comm caller)
   MPI_Comm_rank(comm,&me);
   MPI_Comm_size(comm,&nprocs);
 
-  memory = new Memory(comm);
+  memory = new MemoryLib(comm);
-  error = new Error(comm);
+  error = new ErrorLib(comm);
 
   init();
 

examples/COUPLE/library/irregular.h

@@ -46,8 +46,8 @@ class Irregular {
   MPI_Status *status;        // MPI statuses for Waitall
   MPI_Comm comm;             // MPI communicator for all communication
 
-  class Memory *memory;
+  class MemoryLib *memory;
-  class Error *error;
+  class ErrorLib *error;
 
   void exchange_same(char *, char *);
   void exchange_varying(char *, char *);