Merge branch 'develop' into collected-small-changes

doc/src/Commands_removed.rst

@@ -148,6 +148,14 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
 and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
+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.
+
 restart2data tool
 -----------------
 

doc/src/Fortran.rst

@@ -305,6 +305,8 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype extract_setting: function
    :f extract_global: :f:func:`extract_global`
    :ftype extract_global: function
+   :f map_atom: :f:func:`map_atom`
+   :ftype map_atom: function
    :f extract_atom: :f:func:`extract_atom`
    :ftype extract_atom: function
    :f extract_compute: :f:func:`extract_compute`

doc/src/Library_properties.rst

@@ -13,6 +13,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_extract_setting`
 - :cpp:func:`lammps_extract_global_datatype`
 - :cpp:func:`lammps_extract_global`
+- :cpp:func:`lammps_map_atom`
 
 --------------------
 
@@ -120,3 +121,8 @@ subdomains and processors.
 .. doxygenfunction:: lammps_extract_global
    :project: progguide
 
+-----------------------
+
+.. doxygenfunction:: lammps_map_atom
+   :project: progguide
+

doc/src/Tools.rst

@@ -90,7 +90,7 @@ Miscellaneous tools
 
    * :ref:`LAMMPS coding standards <coding_standard>`
    * :ref:`emacs <emacs>`
-   * :ref:`i-pi <ipi>`
+   * :ref:`i-PI <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS GUI <lammps_gui>`
@@ -376,21 +376,40 @@ See README file in the tools/fep directory.
 
 .. _ipi:
 
-i-pi tool
+i-PI tool
 -------------------
 
-The tools/i-pi directory contains a version of the i-PI package, with
-all the LAMMPS-unrelated files removed.  It is provided so that it can
-be used with the :doc:`fix ipi <fix_ipi>` command to perform
-path-integral molecular dynamics (PIMD).
+.. versionchanged:: TBD
+
+The tools/i-pi directory used to contain a bundled version of the i-PI
+software package for use with LAMMPS.  This version, however, was
+removed in 06/2024.
 
 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.
 
-See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
-:doc:`fix ipi <fix_ipi>` page for further details on running PIMD
-calculations with LAMMPS.
+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
+i-PI into it with all its dependencies.
+
+.. code-block:: sh
+
+   python -m venv ipienv
+   source ipienv/bin/activate
+   pip install --upgrade pip
+   pip install ipi
+
+To install the development version from GitHub, please use:
+
+.. code-block:: sh
+
+   pip install git+https://github.com/i-pi/i-pi.git
+
+For further information, please consult the [i-PI home
+page](https://ipi-code.org).
 
 ----------
 

doc/src/fix_ipi.rst

@@ -79,10 +79,16 @@ setting the *reset* switch.
 Obtaining i-PI
 """"""""""""""
 
-A simple version of the i-PI package, containing only files needed for use
-with LAMMPS, is provided in the tools/i-pi directory. We recommend you
-obtain the latest stable version from the github repository of i-PI,
-or from the python package index.
+Here are the commands to set up a virtual environment and install
+i-PI into it with all its dependencies via the PyPi repository and
+the pip package manager.
+
+.. code-block:: sh
+
+   python -m venv ipienv
+   source ipienv/bin/activate
+   pip install --upgrade pip
+   pip install ipi
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
@@ -125,7 +131,7 @@ Related commands
 
 .. _IPICPC2:
 
-**(IPI-CPC-2019)** Kapil et al., Comp Phys Comm 236, 214–223 (2019).
+**(IPI-CPC-2019)** Kapil et al., Comp Phys Comm 236, 214-223 (2019).
 
 
 .. _ipihome: