move group2ndx and ndx2group to new EXTRA-COMMAND package. update docs.

2024-06-10 14:14:36 -04:00
parent f5253eb926
commit d61c94c0f3
14 changed files with 34 additions and 3 deletions
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@ -256,6 +256,7 @@ set(STANDARD_PACKAGES
  DRUDE
  EFF
  ELECTRODE
+  EXTRA-COMMAND
  EXTRA-COMPUTE
  EXTRA-DUMP
  EXTRA-FIX
--- a/cmake/presets/all_off.cmake
+++ b/cmake/presets/all_off.cmake
@ -28,6 +28,7 @@ set(ALL_PACKAGES
  DRUDE
  ELECTRODE
  EFF
+  EXTRA-COMMAND
  EXTRA-COMPUTE
  EXTRA-DUMP
  EXTRA-FIX
--- a/cmake/presets/all_on.cmake
+++ b/cmake/presets/all_on.cmake
@ -30,6 +30,7 @@ set(ALL_PACKAGES
  DRUDE
  ELECTRODE
  EFF
+  EXTRA-COMMAND
  EXTRA-COMPUTE
  EXTRA-DUMP
  EXTRA-FIX
--- a/cmake/presets/mingw-cross.cmake
+++ b/cmake/presets/mingw-cross.cmake
@ -24,6 +24,7 @@ set(WIN_PACKAGES
  DRUDE
  ELECTRODE
  EFF
+  EXTRA-COMMAND
  EXTRA-COMPUTE
  EXTRA-DUMP
  EXTRA-FIX
--- a/cmake/presets/most.cmake
+++ b/cmake/presets/most.cmake
@ -26,6 +26,7 @@ set(ALL_PACKAGES
  DRUDE
  EFF
  ELECTRODE
+  EXTRA-COMMAND
  EXTRA-COMPUTE
  EXTRA-DUMP
  EXTRA-FIX
--- a/cmake/presets/windows.cmake
+++ b/cmake/presets/windows.cmake
@ -22,6 +22,7 @@ set(WIN_PACKAGES
  DRUDE
  EFF
  ELECTRODE
+  EXTRA-COMMAND
  EXTRA-COMPUTE
  EXTRA-DUMP
  EXTRA-FIX
--- a/doc/src/Packages_details.rst
+++ b/doc/src/Packages_details.rst
@ -52,6 +52,7 @@ page gives those details.
   * :ref:`DRUDE <PKG-DRUDE>`
   * :ref:`EFF <PKG-EFF>`
   * :ref:`ELECTRODE <PKG-ELECTRODE>`
+   * :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
   * :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
   * :ref:`EXTRA-DUMP <PKG-EXTRA-DUMP>`
   * :ref:`EXTRA-FIX <PKG-EXTRA-FIX>`
@ -886,6 +887,22 @@ This package has :ref:`specific installation instructions <electrode>` on the

 ----------

+.. _PKG-EXTRA-COMMAND:
+
+EXTRA-COMMAND package
+---------------------
+
+**Contents:**
+
+Additional compute styles that are less commonly used.
+
+**Supporting info:**
+
+* src/EXTRA-COMMAND: filenames -> commands
+* :doc:`general commands <Commands_all>`
+
+----------
+
 .. _PKG-EXTRA-COMPUTE:

 EXTRA-COMPUTE package
--- a/doc/src/Packages_list.rst
+++ b/doc/src/Packages_list.rst
@ -158,6 +158,11 @@ whether an extra library is needed to build and use the package:
     - :doc:`fix electrode/conp <fix_electrode>`
     - PACKAGES/electrode
     - no
+   * - :ref:`EXTRA-COMMAND <PKG-EXTRA-COMMAND>`
+     - additional command styles
+     - :doc:`general commands <Commands_all>`
+     - n/a
+     - no
   * - :ref:`EXTRA-COMPUTE <PKG-EXTRA-COMPUTE>`
     - additional compute styles
     - :doc:`compute <compute>`
--- a/doc/src/group2ndx.rst
+++ b/doc/src/group2ndx.rst
@ -55,11 +55,12 @@ from the index file and restored.
 Restrictions
 """"""""""""

-This command requires that atoms have atom IDs, since this is the
+These commands require that atoms have atom IDs, since this is the
 information that is written to the index file.

-These commands are part of the COLVARS package.  They are only
-enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+These commands are part of the EXTRA-COMMAND package.  They are only
+enabled if LAMMPS was built with that package.  See the
+:doc:`Build package <Build_package>` page for more info.

 Related commands
 """"""""""""""""
--- a/src/EXTRA-COMMAND/group_ndx.cpp
+++ b/src/EXTRA-COMMAND/group_ndx.cpp
--- a/src/EXTRA-COMMAND/group_ndx.h
+++ b/src/EXTRA-COMMAND/group_ndx.h
--- a/src/EXTRA-COMMAND/ndx_group.cpp
+++ b/src/EXTRA-COMMAND/ndx_group.cpp
--- a/src/EXTRA-COMMAND/ndx_group.h
+++ b/src/EXTRA-COMMAND/ndx_group.h
--- a/src/Makefile
+++ b/src/Makefile
@ -74,6 +74,7 @@ PACKAGE = \
 	dpd-smooth \
 	drude \
 	eff \
+	extra-command \
 	extra-compute \
 	extra-dump \
 	extra-fix \
@ -167,6 +168,7 @@ PACKMOST = \
 	dpd-smooth \
 	drude \
 	eff \
+	extra-command \
 	extra-compute \
 	extra-dump \
 	extra-fix \