Apr 18 2023

ESPResSo 4.2.1 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 4.2.0 and 4.2.1. However, some bugs were discovered which can affect simulation results.

We recommend that this release be used for all production simulations. No further bug fix releases will be provided for the 4.2 line.

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.

Added functionality

  • P3M and DipolarP3M can now be used with the hybrid decomposition cell system with 1 MPI rank (#4678).
  • Lattice-Boltzmann can now be used with the N-square and hybrid decomposition cell systems with 2 or more MPI ranks (#4676).

Changed requirements

  • The nbconvert version requirement was bumped to 6.5.1 to patch an XSS vulnerability (#4658).

Improved documentation

  • The user guide now documents how to improve the reproducibility of simulations that have checkpointing enabled (#4677).
  • The user guide now reflects that the lattice-Boltzmann profile observables can be used in parallel (#4583).
  • The active matter tutorial now uses an adequate engine dipole for the swimmer particle (#4585).
  • The error analysis tutorials have been improved (#4597).
  • The tutorials can now be used in VS Code Jupyter (both the desktop and web versions) and the mathematical formula are now correctly displayed (#4531).
  • All ESPResSo-specific CMake options are now documented in the installation chapter of the user guide (#4608).
  • Python package installation instructions no longer feature package version numbers; instead, requirements.txt is used as a constraint file (#4638).
  • MMM1D algorithms now properly document their parameter names (#4677).
  • Reaction methods now cite the relevant literature (#4681).
  • Caveats for chain analysis methods are now documented (#4698).
  • Minor formatting issues in Sphinx and typos in Python docstrings were addressed (#4608).

Interface changes

  • A new boolean property System.virtual_sites.override_cutoff_check was introduced to allow disabling the cutoff range checks from virtual sites (#4623).

Removed functionality

  • The unused and untested Analysis.v_kappa() method was removed (#4534).

Improved testing

  • Improve unit testing of core functionality: P3M, MMM1D, OIF, virtual sites, script interface factory (#4631).

Bug fixes

  • The checkpointing mechanism now properly restores the particle quaternion and all derived quantities (#4637). Release 4.2.0 introduced a regression that caused checkpoint files to overwrite the particle quaternion/director by a unit vector pointing along the z direction, when the DIPOLES feature was part of the myconfig file. This lead to incorrect trajectories when reloading a simulation from a checkpoint file, if the particle director played a role in the simulation (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). In addition, the angular velocity in body frame was restored with the wrong orientation. Since the default myconfig file contains DIPOLES, most ESPResSo users were affected.
  • The checkpointing mechanism now properly restores LB boundaries (#4649). Release 4.2.0 introduced a regression where reloading LB populations would accidentally reset LB boundary flags.
  • The checkpointing mechanism now restores P3M and DipolarP3M solvers without triggering a re-tune (#4677). In previous releases, the checkpointing code would automatically re-tune these algorithms during a reload, causing tiny deviations in the forces that were problematic for trajectory reproducibility.
  • Brownian dynamics now integrates the rotational dynamics of rotatable particles whose position is fixed in 3D space (#4548).
  • Langevin dynamics now properly integrates particles with anisotropic friction (#4683, #4690).
  • A regression that caused virtual sites to incorrectly count their image box when crossing a periodic boundary has been fixed (#4564, #4707).
  • Particles can no longer be created or updated with a negative mass or a null mass (#4679).
  • Particles created without a user-specified type can now participate in reactions (#4589).
  • When a Monte Carlo displacement move is rejected, the original particle velocity is now restored (#4589).
  • Reaction methods now raise an exception when accidentally calling method.reaction(steps=20) instead of method.reaction(reaction_steps=20) (#4666). Since 4.2.0 the steps argument was ignored, in which case the default value reaction_steps=1 would used by the core. Note that in the next minor release of ESPResSo, the reaction_steps argument will be renamed to steps.
  • Reaction methods now rebuild the list of free particle ids every time WidomInsertion::calculate_particle_insertion_potential_energy() and ReactionAlgorithm::do_reaction() are called (#4609). This was needed to allow multiple concurrent reactions, as well as avoiding subtle bugs when both the user and a reaction method tried to create a new particle with an id that used to belong to a deleted particle.
  • When all particles are cleared, the reaction methods type map is now also cleared (#4645). In the past, it was possible to attempt a reaction on particles that had just been cleared from the system, which would raise an exception. This bug affected all ESPResSo releases since 4.0.
  • The System.part.pairs() method now returns the correct particle pairs when particle ids aren’t both contiguous and starting from 0 (#4628). The regression was introduced in release 4.2.0.
  • The auto-exclusions feature no longer adds spurious exclusions to particle ids in the range 1, distance. This bug would potentially break the physics of the system and potentially raise an exception in a system with non-contiguous particle ids. This regression was introduced in release 2.2.0b.
  • The structure factor analysis code no longer double-counts particles when the same particle type is provided twice (#4534).
  • The minimal distance distribution analysis code no longer has an arbitrary cutoff distance when the simulation box is aperiodic (open boundaries); this would cause spurious artifacts to appear in the histogram at r = np.sum(system.box_l) when particles were further apart than this arbitrary distance (#4534).
  • The cluster analysis functions are now disabled for systems with Lees-Edwards periodic boundaries, since the cluster analysis position wrapping code doesn’t properly handle the shear offset (#4698).
  • The chain analysis methods now raise an error when the number of chains or beads per chain is invalid (#4708).
  • The observable tests now longer rely on deprecated numpy options that were removed in numpy 1.24 (#4635).
  • The visualizer *_arrows_type_materials options now have an effect on arrow materials (#4686).
  • The visualizer exception handling mechanism has been made less brittle (#4686).
  • The visualizer no longer raises exception when the optional dependency freeglut isn’t installed (#4691).
  • The visualizer can randomly freeze when using collision detection or bond breakage; a temporary workaround has been introduced that fixes the issue for simulations that use only 1 MPI rank (#4686).
  • The __dir__() method of script interface objects no longer raises an exception (#4674).
  • Compilation and testsuite issues involving missing or incorrect feature guards were addressed (#4562, #4648).
  • The build system no longer silently ignores invalid external feature definitions in myconfig.hpp and CMake files (#4608). This issue would only affect feature developers, as well as users of very old compilers, and would lead to ESPResSo builds missing features.

Under the hood changes

  • The Clang 14 and AppleClang 14 compilers are now supported (#4601).
  • Several Clang 14 compiler diagnostics have been addressed (#4606).
  • Boost 1.81 and later versions are now supported (#4655).
  • Compiler errors on non-x86 architectures were addressed (#4538).
  • Test tolerances were adjusted for non-x86 architectures (#4708).
  • The pypresso script now prints a warning when running with MCA binding policy “numa” on NUMA architectures that are not supported in singleton mode by Open MPI 4.x (#4607).
  • The config file generator has been rewritten to properly handle external features and compiler errors (#4608).
  • Security hardening for GitHub Workflows (#4577, #4638) and Codecov (#4600).
  • Deployment of the user guide to GitHub Pages now relies on cloud providers to fetch JavaScript dependencies (#4656).

jngrad