May 22 2024

ESPResSo 4.2.2 released

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.

Please find the list of changes below. The numbers in brackets refer to ticket numbers on https://github.com/espressomd/espresso

Get the source code in the Download area.

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).
  • 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).

jngrad