Merge pull request lammps#4203 from akohlmey/collected-small-changes

Collected small changes and bugfixes

.github/CODEOWNERS

@@ -59,7 +59,8 @@ src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
-src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane @stanmoore1
+src/KOSSOS/pair_pod_kokkos.*        @exapde @stanmoore1
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/MANYBODY/pair_nb3b_screened.*   @flodesani

.gitignore

@@ -43,12 +43,12 @@ Thumbs.db
 
 #cmake
 /build*
-/CMakeCache.txt
-/CMakeFiles/
-/Testing
+CMakeCache.txt
+CMakeFiles
 /Makefile
-/Testing
-/cmake_install.cmake
+Testing
+Temporary
+cmake_install.cmake
 /lmp
 out/Debug
 out/RelWithDebInfo

cmake/CMakeLists.txt

@@ -23,6 +23,7 @@ project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
+include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -208,7 +209,7 @@ else()
   unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
-include(GNUInstallDirs)
+
 file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
@@ -282,10 +283,10 @@ set(STANDARD_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-POD
   ML-UF3
   MOFFF
   MOLECULE

cmake/presets/all_off.cmake

@@ -26,8 +26,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP

cmake/presets/all_on.cmake

@@ -28,8 +28,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP

cmake/presets/mingw-cross.cmake

@@ -22,8 +22,8 @@ set(WIN_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
   EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP

cmake/presets/windows.cmake

@@ -52,8 +52,8 @@ set(WIN_PACKAGES
   ORIENT
   PERI
   PHONON
-  POEMS
   PLUGIN
+  POEMS
   PTM
   QEQ
   QTB

doc/src/Commands_removed.rst

@@ -154,7 +154,7 @@ i-PI tool
 .. versionchanged:: TBD
 
 The i-PI tool has been removed from the LAMMPS distribution.  Instead,
-instructions to install i-PI from PyPi via pip are provided.
+instructions to install i-PI from PyPI via pip are provided.
 
 restart2data tool
 -----------------

doc/src/Developer_utils.rst

@@ -211,6 +211,9 @@ Argument processing
 .. doxygenfunction:: bounds
    :project: progguide
 
+.. doxygenfunction:: bounds_typelabel
+   :project: progguide
+
 .. doxygenfunction:: expand_args
    :project: progguide
 

doc/src/Tools.rst

@@ -389,7 +389,7 @@ The i-PI package was created and is maintained by Michele Ceriotti,
 michele.ceriotti at gmail.com, to interface to a variety of molecular
 dynamics codes.
 
-i-PI is now available via PyPi using the pip package manager at:
+i-PI is now available via PyPI using the pip package manager at:
 https://pypi.org/project/ipi/
 
 Here are the commands to set up a virtual environment and install
@@ -839,7 +839,7 @@ and LAMMPS GUI can be launched from anywhere from the command line.
 
 The standard CMake build procedure can be applied and the
 ``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
-command will automatically include a suitable CMake toolset file (the
+command will automatically include a suitable CMake toolchain file (the
 regular cmake command can be used after that to modify the configuration
 settings, if needed).  After building the libraries and executables,
 you can build the target 'zip' (i.e. ``cmake --build <build dir> --target zip``

doc/src/compute_pod_atom.rst

@@ -10,10 +10,10 @@ compute podd/atom command
 =========================
 
 compute pod/local command
-=======================
+=========================
 
 compute pod/global command
-=======================
+==========================
 
 Syntax
 """"""
@@ -47,44 +47,63 @@ Examples
 Description
 """""""""""
 
+.. versionadded:: 27June2024
+
 Define a computation that calculates a set of quantities related to the
 POD descriptors of the atoms in a group. These computes are used
 primarily for calculating the dependence of energy and force components
-on the linear coefficients in the :doc:`pod pair_style
-<pair_pod>`, which is useful when training a POD potential to match
-target data. POD descriptors of an atom are characterized by the
-radial and angular distribution of neighbor atoms. The detailed
-mathematical definition is given in the papers by :ref:`(Nguyen and Rohskopf) <Nguyen20222>`,
-:ref:`(Nguyen2023) <Nguyen20232>`, :ref:`(Nguyen2024) <Nguyen20242>`, and :ref:`(Nguyen and Sema) <Nguyen20243>`.
+on the linear coefficients in the :doc:`pod pair_style <pair_pod>`,
+which is useful when training a POD potential to match target data. POD
+descriptors of an atom are characterized by the radial and angular
+distribution of neighbor atoms. The detailed mathematical definition is
+given in the papers by :ref:`(Nguyen and Rohskopf) <Nguyen20222c>`,
+:ref:`(Nguyen2023) <Nguyen20232c>`, :ref:`(Nguyen2024) <Nguyen20242c>`,
+and :ref:`(Nguyen and Sema) <Nguyen20243c>`.
 
 Compute *pod/atom* calculates the per-atom POD descriptors.
 
-Compute *podd/atom* calculates derivatives of the per-atom POD descriptors with respect to atom positions.
+Compute *podd/atom* calculates derivatives of the per-atom POD
+descriptors with respect to atom positions.
+
+Compute *pod/local* calculates the per-atom POD descriptors and their
+derivatives with respect to atom positions.
+
+Compute *pod/global* calculates the global POD descriptors and their
+derivatives with respect to atom positions.
+
+Examples how to use Compute POD commands are found in the directory
+``examples/PACKAGES/pod``.
 
-Compute *pod/local* calculates the per-atom POD descriptors and their derivatives with respect to atom positions.
 
-Compute *pod/global* calculates the global POD descriptors and their derivatives with respect to atom positions.
+.. warnings::
 
-Examples how to use Compute POD commands are found in the directory lammps/examples/PACKAGES/pod.
+   All of these compute styles produce *very* large per-atom output
+   arrays that scale with the total number of atoms in the system.
+   This will result in *very* large memory consumption for systems
+   with a large number of atoms.
 
 ----------
 
 Output info
 """""""""""
 
-Compute *pod/atom* produces an 2D array of size :math:`N \times M`, where :math:`N` is the number of atoms
-and :math:`M` is the number of descriptors. Each column corresponds to a particular POD descriptor.
+Compute *pod/atom* produces an 2D array of size :math:`N \times M`,
+where :math:`N` is the number of atoms and :math:`M` is the number of
+descriptors. Each column corresponds to a particular POD descriptor.
 
-Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3 N)`. Each column
-corresponds to a particular derivative of a POD descriptor.
+Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3
+N)`. Each column corresponds to a particular derivative of a POD
+descriptor.
 
-Compute *pod/local* produces an 2D array of size :math:`(1 + 3N) \times (M * N)`.
-The first row contains the per-atom descriptors, and the last 3N rows contain the derivatives
-of the per-atom descriptors with respect to atom positions.
+Compute *pod/local* produces an 2D array of size :math:`(1 + 3N) \times
+(M * N)`.  The first row contains the per-atom descriptors, and the last
+3N rows contain the derivatives of the per-atom descriptors with respect
+to atom positions.
 
-Compute *pod/global* produces an 2D array of size :math:`(1 + 3N) \times (M)`.
-The first row contains the global descriptors, and the last 3N rows contain the derivatives
-of the global descriptors with respect to atom positions.
+Compute *pod/global* produces an 2D array of size :math:`(1 + 3N) \times
+(M)`.  The first row contains the global descriptors, and the last 3N
+rows contain the derivatives of the global descriptors with respect to
+atom positions.
 
 Restrictions
 """"""""""""
@@ -107,19 +126,19 @@ none
 
 ----------
 
-.. _Nguyen20222:
+.. _Nguyen20222c:
 
 **(Nguyen and Rohskopf)** Nguyen and Rohskopf,  Journal of Computational Physics, 480, 112030, (2023).
 
-.. _Nguyen20232:
+.. _Nguyen20232c:
 
 **(Nguyen2023)** Nguyen, Physical Review B, 107(14), 144103, (2023).
 
-.. _Nguyen20242:
+.. _Nguyen20242c:
 
 **(Nguyen2024)** Nguyen, Journal of Computational Physics, 113102, (2024).
 
-.. _Nguyen20243:
+.. _Nguyen20243c:
 
 **(Nguyen and Sema)** Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).