From d61c94c0f3634fd6cc68fb1fdcd41f45fa25bf61 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 10 Jun 2024 14:14:36 -0400 Subject: [PATCH] move group2ndx and ndx2group to new EXTRA-COMMAND package. update docs. --- cmake/CMakeLists.txt | 1 + cmake/presets/all_off.cmake | 1 + cmake/presets/all_on.cmake | 1 + cmake/presets/mingw-cross.cmake | 1 + cmake/presets/most.cmake | 1 + cmake/presets/windows.cmake | 1 + doc/src/Packages_details.rst | 17 +++++++++++++++++ doc/src/Packages_list.rst | 5 +++++ doc/src/group2ndx.rst | 7 ++++--- src/{COLVARS => EXTRA-COMMAND}/group_ndx.cpp | 0 src/{COLVARS => EXTRA-COMMAND}/group_ndx.h | 0 src/{COLVARS => EXTRA-COMMAND}/ndx_group.cpp | 0 src/{COLVARS => EXTRA-COMMAND}/ndx_group.h | 0 src/Makefile | 2 ++ 14 files changed, 34 insertions(+), 3 deletions(-) rename src/{COLVARS => EXTRA-COMMAND}/group_ndx.cpp (100%) rename src/{COLVARS => EXTRA-COMMAND}/group_ndx.h (100%) rename src/{COLVARS => EXTRA-COMMAND}/ndx_group.cpp (100%) rename src/{COLVARS => EXTRA-COMMAND}/ndx_group.h (100%) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f87c92396f..6421f5356f 100644 --- 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 diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index e078879f70..50a0bf846c 100644 --- 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 diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 3f44a863f7..52a2a3a753 100644 --- 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 diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index f3565668b2..49e81868ae 100644 --- 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 diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 2356e24764..c539ea1d3d 100644 --- 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 diff --git a/cmake/presets/windows.cmake b/cmake/presets/windows.cmake index 9655134e7f..360f26cb90 100644 --- 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 diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index a3d65d9d65..d96d73bcce 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -52,6 +52,7 @@ page gives those details. * :ref:`DRUDE ` * :ref:`EFF ` * :ref:`ELECTRODE ` + * :ref:`EXTRA-COMMAND ` * :ref:`EXTRA-COMPUTE ` * :ref:`EXTRA-DUMP ` * :ref:`EXTRA-FIX ` @@ -886,6 +887,22 @@ This package has :ref:`specific installation instructions ` 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 ` + +---------- + .. _PKG-EXTRA-COMPUTE: EXTRA-COMPUTE package diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index c0a1164513..34d6aff393 100644 --- 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 ` - PACKAGES/electrode - no + * - :ref:`EXTRA-COMMAND ` + - additional command styles + - :doc:`general commands ` + - n/a + - no * - :ref:`EXTRA-COMPUTE ` - additional compute styles - :doc:`compute ` diff --git a/doc/src/group2ndx.rst b/doc/src/group2ndx.rst index 077f88e3e8..8c28d43aa0 100644 --- 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 ` 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 ` page for more info. Related commands """""""""""""""" diff --git a/src/COLVARS/group_ndx.cpp b/src/EXTRA-COMMAND/group_ndx.cpp similarity index 100% rename from src/COLVARS/group_ndx.cpp rename to src/EXTRA-COMMAND/group_ndx.cpp diff --git a/src/COLVARS/group_ndx.h b/src/EXTRA-COMMAND/group_ndx.h similarity index 100% rename from src/COLVARS/group_ndx.h rename to src/EXTRA-COMMAND/group_ndx.h diff --git a/src/COLVARS/ndx_group.cpp b/src/EXTRA-COMMAND/ndx_group.cpp similarity index 100% rename from src/COLVARS/ndx_group.cpp rename to src/EXTRA-COMMAND/ndx_group.cpp diff --git a/src/COLVARS/ndx_group.h b/src/EXTRA-COMMAND/ndx_group.h similarity index 100% rename from src/COLVARS/ndx_group.h rename to src/EXTRA-COMMAND/ndx_group.h diff --git a/src/Makefile b/src/Makefile index b9f1bcbdef..b56631a46a 100644 --- 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 \