[pull] develop from lammps:develop #83

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Merged

pull merged 17 commits into comphy-lab:develop from lammps:develop

Dec 20, 2025

+141 −144

doc/src/Packages_details.rst

            
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    @@ -1054,8 +1054,8 @@ This package has :ref:`specific installation instructions <gpu>` on the
  
    * ``lib/gpu/README``

    * :doc:`Accelerator packages <Speed_packages>`

    * :doc:`GPU package <Speed_gpu>`

    * :doc:`Section 2.6 -sf gpu <Run_options>`

    * :doc:`Section 2.6 -pk gpu <Run_options>`

    * :doc:`Section 4.2 -sf gpu <Run_options>`

    * :doc:`Section 4.2 -pk gpu <Run_options>`

    * :doc:`package gpu <package>`

    * :doc:`Commands <Commands_all>` pages (:doc:`pair <Commands_pair>`, :doc:`kspace <Commands_kspace>`)

      for styles followed by (g)

    @@ -1165,8 +1165,8 @@ This package has :ref:`specific installation instructions <intel>` on the :doc:`
  
    * ``src/INTEL/README``

    * :doc:`Accelerator packages <Speed_packages>`

    * :doc:`INTEL package <Speed_intel>`

    * :doc:`Section 2.6 -sf intel <Run_options>`

    * :doc:`Section 2.6 -pk intel <Run_options>`

    * :doc:`Section 4.2 -sf intel <Run_options>`

    * :doc:`Section 4.2 -pk intel <Run_options>`

    * :doc:`package intel <package>`

    * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,

      :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`, :doc:`kspace <Commands_kspace>`) for styles followed by (i)

    @@ -1302,9 +1302,9 @@ This package has :ref:`specific installation instructions <kokkos>` on the :doc:
  
    * ``lib/kokkos/README``

    * :doc:`Accelerator packages <Speed_packages>`

    * :doc:`KOKKOS package <Speed_kokkos>`

    * :doc:`Section 2.6 -k on ... <Run_options>`

    * :doc:`Section 2.6 -sf kk <Run_options>`

    * :doc:`Section 2.6 -pk kokkos <Run_options>`

    * :doc:`Section 4.2 -k on ... <Run_options>`

    * :doc:`Section 4.2 -sf kk <Run_options>`

    * :doc:`Section 4.2 -pk kokkos <Run_options>`

    * :doc:`package kokkos <package>`

    * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,

      :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,

    @@ -2203,7 +2203,7 @@ This package has :ref:`specific installation instructions <opt>` on the :doc:`Bu
  
    * ``src/OPT``: filenames -> commands

    * :doc:`Accelerator packages <Speed_packages>`

    * :doc:`OPT package <Speed_opt>`

    * :doc:`Section 2.6 -sf opt <Run_options>`

    * :doc:`Section 4.2 -sf opt <Run_options>`

    * Search the :doc:`pair style <Commands_pair>` page for styles followed by (t)

    * `Benchmarks page <https://www.lammps.org/bench.html>`_ of website

doc/src/Speed_packages.rst

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@@ Expand Up / @@ -101,7 +101,7 @@ listed above. @@
     +-----------------------------------------------------------+---------------------------------------------+
     This is discussed on the :doc:`Packages <Packages>` and :doc:`extra
-    Build info <Build_extra>` doc pages, and its use is illustrated in the
+    Build info <Build_extras>` doc pages, and its use is illustrated in the
     individual accelerator sections.  Typically these steps only need to be
     done once, to create an executable that uses one or more accelerator
     packages.
@@ Expand Down @@

doc/src/angle_zero.rst

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     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
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doc/src/bond_none.rst

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@@ Expand Up / @@ -29,7 +29,7 @@ calculate bond statistics, but compute no bond interactions. @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/bond_zero.rst

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@@ Expand Up @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
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doc/src/compute_angle_local.rst

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@@ Expand Up / @@ -138,7 +138,7 @@ be in energy :doc:`units <units>`. @@
     Restrictions
     """"""""""""
-     none
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     """"""""""""""""
@@ Expand Down @@

doc/src/compute_angmom_chunk.rst

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@@ Expand Up / @@ -83,7 +83,7 @@ mass-velocity-distance :doc:`units <units>`. @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_body_local.rst

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@@ Expand Up @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_bond.rst

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@@ Expand Up / @@ -49,7 +49,7 @@ The vector values are "extensive" and will be in energy @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_bond_local.rst

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@@ Expand Up / @@ -20,7 +20,6 @@ Syntax @@
          *dist* = bond distance
          *engpot* = bond potential energy
          *force* = bond force
          *dx*,\ *dy*,\ *dz* = components of pairwise distance
          *fx*,\ *fy*,\ *fz* = components of bond force
          *engvib* = bond kinetic energy of vibration
@@ Expand All / @@ -47,9 +46,7 @@ Examples @@
        compute 1 all bond/local engpot
        compute 1 all bond/local dist engpot force
        compute 1 all bond/local dist fx fy fz b1 b2
        compute 1 all bond/local dist v_distsq set dist d
     Description
@@ Expand Down Expand Up @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_centro_atom.rst

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@@ Expand Up / @@ -150,7 +150,7 @@ of 12. @@
     Restrictions
     """"""""""""
-     none
+    none
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@@ Expand Down @@

doc/src/compute_chunk_spread_atom.rst

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@@ Expand Up / @@ -206,7 +206,7 @@ The vector or array values are "intensive". @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_cna_atom.rst

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@@ Expand Up / @@ -94,7 +94,7 @@ above. @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_com.rst

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@@ Expand Up / @@ -54,7 +54,7 @@ distance :doc:`units <units>`. @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_com_chunk.rst

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@@ Expand Up / @@ -82,7 +82,7 @@ distance :doc:`units <units>`. @@
     Restrictions
     """"""""""""
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_coord_atom.rst

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@@ Expand Up / @@ -140,7 +140,7 @@ explained above. @@
     Restrictions
     """"""""""""
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@@ Expand Down @@

doc/src/compute_dihedral.rst

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@@ Expand Up / @@ -47,7 +47,7 @@ The vector values are "extensive" and will be in energy @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_dihedral_local.rst

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@@ Expand Up / @@ -131,7 +131,7 @@ The output for *phi* will be in degrees. @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_displace_atom.rst

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@@ Expand Up / @@ -139,7 +139,7 @@ incremental dump files. @@
     Restrictions
     """"""""""""
-     none
+    none
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     """"""""""""""""
@@ Expand Down @@

doc/src/compute_erotate_sphere_atom.rst

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@@ Expand Up @@
     Restrictions
     """"""""""""
-     none
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doc/src/compute_global_atom.rst

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@@ Expand Up / @@ -225,7 +225,7 @@ corresponding input values are in. @@
     Restrictions
     """"""""""""
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@@ Expand Down @@

doc/src/compute_gyration.rst

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@@ Expand Up / @@ -74,7 +74,7 @@ distance\ :math:`^2` :doc:`units <units>`, respectively. @@
     Restrictions
     """"""""""""
-     none
+    none
     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_gyration_chunk.rst

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@@ Expand Up / @@ -115,7 +115,7 @@ represented by the formula above. @@
     Restrictions
     """"""""""""
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     """"""""""""""""
@@ Expand Down @@

doc/src/compute_heat_flux.rst

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@@ Expand Up / @@ -157,7 +157,7 @@ energy/area/time :doc:`units <units>` @@
     Restrictions
     """"""""""""
-     none
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     Related commands
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@@ Expand Down @@

doc/src/compute_improper.rst

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@@ Expand Up / @@ -47,7 +47,7 @@ The vector values are "extensive" and will be in energy @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_improper_local.rst

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@@ Expand Up / @@ -77,7 +77,7 @@ The output for *chi* will be in degrees. @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_inertia_chunk.rst

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@@ Expand Up / @@ -89,7 +89,7 @@ mass\*distance\ :math:`^2` :doc:`units <units>`. @@
     Restrictions
     """"""""""""
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_ke.rst

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@@ Expand Up / @@ -57,7 +57,7 @@ scalar value will be in energy :doc:`units <units>`. @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_ke_atom.rst

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     Restrictions
     """"""""""""
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doc/src/compute_modify.rst

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@@ Expand Up / @@ -60,7 +60,7 @@ temperature is correctly normalized. @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_msd_chunk.rst

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@@ Expand Up / @@ -126,7 +126,7 @@ distance\ :math:`^2` :doc:`units <units>`. @@
     Restrictions
     """"""""""""
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     Related commands
     """"""""""""""""
@@ Expand Down @@

doc/src/compute_omega_chunk.rst

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@@ Expand Up / @@ -89,7 +89,7 @@ velocity/distance :doc:`units <units>`. @@
     Restrictions
     """"""""""""
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     """"""""""""""""
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doc/src/compute_pair.rst

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@@ Expand Up / @@ -88,7 +88,7 @@ the page for the pair style for details. @@
     Restrictions
     """"""""""""
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doc/src/compute_pair_local.rst

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     Restrictions
     """"""""""""
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doc/src/compute_pe.rst

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@@ Expand Up / @@ -78,7 +78,7 @@ scalar value will be in energy :doc:`units <units>`. @@
     Restrictions
     """"""""""""
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     """"""""""""""""
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doc/src/compute_pressure.rst

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     Restrictions
     """"""""""""
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doc/src/compute_property_atom.rst

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@@ Expand Up / @@ -215,7 +215,7 @@ are given in rad/THz. @@
     Restrictions
     """"""""""""
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     """"""""""""""""
@@ Expand Down @@

doc/src/compute_property_chunk.rst

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@@ Expand Up / @@ -118,7 +118,7 @@ unitless or in the units discussed above. @@
     Restrictions
     """"""""""""
-     none
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     Related commands
     """"""""""""""""
@@ Expand Down @@

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