ESPResSo 4.2.2 released

[Jean-Noël Grad]

Dear users,

The ESPResSo team is pleased to announce the release of ESPResSo 4.2.2. 
The sources can be downloaded at 
https://github.com/espressomd/espresso/releases/download/4.2.2/espresso-4.2.2.tar.gz
Please see the release notes below.

The release has been submitted to Fedora 39 [1], Fedora 40 [2], Fedora 
41 [3], openSUSE Tumbleweed [4], EasyBuild [5] and EESSI [6]. The user 
guide [7] and tutorials [8] are available online.

Many thanks to all contributors!

Best regards,
Jean-Noël Grad

Links:
[1] https://bodhi.fedoraproject.org/updates/FEDORA-2024-3dbcf568b4
[2] https://bodhi.fedoraproject.org/updates/FEDORA-2024-a586fb0197
[3] https://bodhi.fedoraproject.org/updates/FEDORA-2024-6f8e4a356f
[4] https://build.opensuse.org/request/show/1175904
[5] https://github.com/easybuilders/easybuild-easyconfigs/pull/20595
[6] https://github.com/EESSI/software-layer/pull/584
[7] https://espressomd.github.io/doc4.2.2/index.html
[8] https://espressomd.github.io/tutorials4.2.2.html

==============

This release provides a number of corrections for the ESPResSo 4.2 line.
We recommend that this release be used for all production simulations.
The interface has not been changed between ESPResSo 4.2.1 and 4.2.2.
However, some bugs were discovered which can affect simulation results.
In addition, the checkpointing mechanism is now fully functional again.
Please find the list of changes below. The numbers in brackets refer to
ticket numbers on https://github.com/espressomd/espresso

Improved documentation
----------------------

* Installation instructions now mention the FFTW3 MPI dependency of 
long-range solvers and provide recommended version numbers for Jupyter 
Notebook dependencies (#4790).

* Installation instructions now mention Python environments (#4922). 
More details can be found in the wiki: 
https://github.com/espressomd/espresso/wiki/Tooling#environments

* Observables not properly document return values, array shapes, and use 
a more consistent mathematical notation (#4898).

Bug fixes
---------

* Fatal runtime errors due to MPI global variables lifetime were 
addressed (#4858). Older ESPResSo releases built with Boost 1.84 or 
later might randomly crash when exiting the Python interpreter.

* Virtual sites no longer contribute to the kinetic energy of the system 
(#4839). The regression was introduced in April 2021 and affected the 
4.2 branch of ESPResSo.

* Inertialess tracers are now integrated along the z-axis (#4714). The 
regression was introduced in February 2022 and affected the 4.2 branch 
of ESPResSo.

* Inertialess tracers now throw an exception when attempting to use LB 
GPU with 2 or more MPI ranks (#4714). Before, tracers on non-root MPI 
ranks would be silently ignored by the CUDA kernels, and would have a 
constant velocity, either 0 if the particle never visited the fluid 
domain on the root rank, or the last known velocity if the particle was 
once on the root rank. This bug affected all ESPResSo versions.

* Particles close to the faces of the simulation box are now properly 
coupled to the LB fluid (#4827). Due to numerical instability, it was 
previously possible for particles to be outside the box simulation by a 
tiny amount and skip LB particle coupling. The probability of this bug 
occurring was low, but could be enhanced in simulations that 
purposefully placed particle near the faces of the simulation box: 
polymers sheared by Lees-Edwards boundary conditions, raspberry 
particles (colloids, bacteria, etc.) when crossing a periodic boundary, 
or cell membranes placed close to a periodic boundary.

* Resizing the box now throws a runtime error if there are constraints 
present (#4778), since constraint preconditions might no longer be 
fulfilled. For example, a wall constraint might end up outside the box 
boundaries when the box shrinks.

* Resizing the box via `system.box_l = new_box_l` now throws a runtime 
error if there are particles present, because particle position folding 
cannot be guaranteed to be correct (#4901); use 
`system.change_volume_and_rescale_particles()` instead, which properly 
rescales particle positions.

* The velocity Verlet NpT propagator doesn't apply friction and noise on 
angular velocities. ESPResSo now throws an error when NpT encounters a 
rotating particle (#4843). This bug affected all ESPResSo versions.

* The Brownian thermostat can no longer be configured with 
`act_on_virtual=True` due to an unresolved bug (#4295) that will be 
addressed in the next minor release.

* Restrictions on the number of MPI ranks have been lifted from the 
checkpointing mechanism (#4724). It is now possible to use checkpointing 
again in MPI-parallel simulations when the system contains LB boundaries 
or `Union` shape-based constraints. These restrictions had been 
introduced in 4.2.0 for technical reasons that have since been resolved.

* When passing an invalid value to a function that expects an input 
parameter of type `list` of size 3, an exception is now raised (#4911). 
Previously, some functions would print an error message and continue 
their execution with uninitialized data.

* The per-`type` and per-`mol_id` contributions from 
`system.analysis.energy()`, `system.analysis.pressure()` and 
`system.analysis.pressure_tensor()` now return the correct values 
(#4788). Older version of ESPResSo were confusing the particle `mol_id` 
with the particle `type`. The total pressure was unreliable when 
`mol_id` properties were set to non-zero values.

* The OpenGL visualizer now extracts the correct non-bonded potential 
parameter `sigma` when feature `WCA` is compiled in but `LENNARD_JONES` 
isn't (#4720). The regression was introduced in 4.2.1.

* Method `OifCell.elastic_forces()` no longer throws a `TypeError` (#4813).

* Benchmark scripts were adjusted to support large particle numbers (#4753).

Under the hood changes
----------------------

* Several Clang 16 and GCC 13 compiler diagnostics have been addressed 
(#4715).

* A non-critical GCC C++20 deprecation warning in Cython-generated code 
was disabled (#4725).

* Several deprecation warnings emitted by CMake 3.27 have been silenced 
(#4792).

* Add support for setuptools version 67.3.0 and above (#4709).

* Add support for Python 3.12 in testsuites run by CTest (#4852).

* Python requirements have been updated (#4924).

* CI pipeline URLs have been fixed (#4736).