Dec 13 2019

ESPResSo 4.1.2 released

This release provides a number of corrections for the ESPResSo 4.1 line. We recommend that this release be used for all production simulations. The interface has not been changed between ESPResSo 4.1.1 and 4.1.2. However, some bugs were discovered which can affect simulation results. Below, please find the list of changes. The numbers in brackets refer to ticket numbers on https://github.com/espressomd/espresso

General corrections and improvements:

  • Remove correlation between the rotational noise and translational noise in the Langevin thermostat (#3355)
  • Fix a bug that may cause the wrong temperature to be set by the Langevin and DPD thermostats in the first time step after the system was altered from the Python level, e.g., by changing particles or interactions (#3341)
  • Fix a bug that caused the DPD thermostat to generate an incorrect velocity distribution when used together with the Langevin thermostat (#3352)
  • Fix a bug in MMM2D and ELC with potential boundary conditions, where one of the correction factors was over-counted resulting in wrong energies (#3310)
  • Fix a bug that caused the wrong bonds to be deleted when removing particles from the system (#3356)
  • Fix an ambiguity in ParticleSlice: the values in the square brackets refer to particle ids, not array indices (#3367). This means the ill-defined syntax system.part[0:-1] is no longer valid. See the User Guide section on Setting up particles for more information.
  • Remove the mass prefactor in the ComForce observable and use the correct Particle ids in the ParticleAngularVelocities and ParticleBodyVelocities observables (#3380)
  • Fix a rounding error that caused debug builds of ESPResSo running with multiple MPI threads to crash when a particle was placed exactly on the boundary between two cells (#3377)
  • Fix espressomd.has_features() for the corner case where the list of all compiled-in features is passed as argument, returning False instead of True (#3318)
  • Refactor the random number generator code (#3349)
  • Minor fixes (#3351, #3336)

Documentation and tutorials corrections and improvements:

  • Improve documentation of Monte Carlo methods (#3254, #3330)
  • Minor fixes (#3342, #3334)

Build system and platform-related corrections and improvements:

  • List all Python dependencies in requirements.txt with the supported version numbers (#3300). Please note that most of them are optional.
  • Add MPIEXEC_PREFLAGS and MPIEXEC_POSTFLAGS to the command lines of parallel tests (#3221)
  • Add the -oversubscribe flag to the command lines of parallel tests running with OpenMPI v2.X to avoid exiting early from a Python test configured without MAX_NUM_PROC on a machine with a hyperthreaded CPU where OpenMPI is configured such that the number of threads cannot exceed the number of cores (#3335)
  • Refactor the CI, maintainer, Doxygen and pypresso shell scripts to make them more portable and support filepaths containing whitespaces (#3326, #3373)
  • Fix a nvcc compiler warning on the empty config (#3329)

Improved testing:

  • Add a test for ELC and MMM2D using analytic expressions of the force and energy (#3331)
  • Sped-up seven Python tests (#3319)
  • Fix a test that broke on s390x architectures with Fedora 31 (#3312)
  • Fix tests that broke on i586 architectures with OpenSUSE Tumbleweed (#3327, #3358)

jngrad