Skip to content

4.1.1
Compare
Choose a tag to compare
@jngrad jngrad released this 13 Nov 14:34
· 368 commits to 4.1 since this release
4.1.1
2b7157a
This commit was signed with the committer’s verified signature.
jngrad Jean-Noël Grad
GPG key ID: F1AD0CB8BBD1F049
Learn about vigilant mode.

This bugfix release provides a number of corrections for the ESPResSo 4.1 line.

The interface is mostly unchanged between ESPResSo 4.1.0 and 4.1.1; the two exceptions are limited to these experimental features:

  • Integrator.set_isotropic_npt(): input value direction=[0,0,0] now throws an error instead of being silently changed to [1,1,1]
  • ParticleHandle.swimming: deprecated value 'rotational_friction' is now disabled

These changes are unlikely to affect production simulations.

General corrections and improvements:

  • Restore checkpointing mechanism for the steepest descent and NPT integrators, LB and NPT thermostats (#3245)
  • Increase the minimum MPI version to 3.0; OpenMPI versions 1.6.5 and lower are no longer supported (#3236)
  • Fix Integrator.set_isotropic_npt(): remove the silent conversion of the incorrect input parameter direction=[0,0,0] to [1,1,1] in the core; the function now throws an exception for fixed-volume boxes; this change is unlikely to break pypresso scripts since not providing a value to direction or providing [1,1,1] were the two standard ways to set up a box with all directions allowed to rescale (#3253)
  • Fix Integrator.set_vv(): this function failed to set the velocity Verlet integrator if the NPT integrator was active; this is now resolved (#3274)
  • Fix the random segmentation fault triggered by the removal of a particle with a bond or a virtual site relationship to another particle (#3288)
  • Fix system.part.writevtk(): the function now writes down all particles when using types="all" (#3290)
  • Disable the deprecated and broken ENGINE shear torque calculation feature; the feature will be completely removed from the core in the upcoming 4.2 release (#3277)
  • Fix unit conversion for the LB fluid viscosity (#3287)

Documentation and tutorials corrections and improvements:

  • Add more detailed installation instructions for ESPResSo and its Python dependencies on MacOS X (#3236)
  • Add links to Dockerfiles providing installation instructions for ESPResSo and its Python dependencies on CentOS 7, Fedora 30, Debian 10 and OpenSUSE Leap 15.1 (#3244)
  • Add instructions to read PDB files with MDAnalysis, which is one of the recommended tools to read/write molecular dynamics topologies and trajectories in ESPResSo; the PdbParser feature will be removed in the upcoming 4.2 release (#3257)
  • Add a new tutorial on the constant pH method; the reaction ensemble tutorial will be removed in the upcoming 4.2 release (#3184)

Build system and platform-related corrections and improvements:

  • Fix a PYTHONPATH error when ESPResSo is built in a directory containing whitespace characters (#3238)
  • Fix several issues with the command make install that lead to import errors in Python (incorrect runtime path, missing shared objects, name collision for submodule cluster_analysis) and deprecate the make install DESTDIR=/path/to/espresso command in favor of the standard cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/espresso command (#3228), install espressomd module in a platform-dependent python path, typically lib{,64}/python3.X/{dist,site}-packages (#3258)
  • Fix an issue in mpiio that triggered an assertion in systems with no bonds when ESPResSo is built with stdlibc++ range checking enabled (#3234)
  • Fix the pypresso script to correctly parse filepaths containing whitespaces passed after a pypresso flag, such as --gdb, and make conditional statements cross-platform (#3292)

Improved testing:

  • Test checkpointing of integrators and thermostats (#3245)
  • Fix and improve check_cmake_install test (#3228, #3258) and add a new CI job to test an installed version of ESPResSo (#3228)
  • Test engine LB (#3277)
  • Add more LB tests (#2748)
Assets 4
Loading