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Espresso 4.1.1 released

From: Jean-Noël Grad
Subject: Espresso 4.1.1 released
Date: Wed, 13 Nov 2019 20:32:27 +0100
User-agent: Mozilla/5.0 (X11; Linux i686; rv:60.0) Gecko/20100101 Thunderbird/60.9.0

Dear Espresso users,

The Espresso team is pleased to announce the release of Espresso 4.1.1. The source can be downloaded at
Please see the release notes below.

Many thanks to all contributors!
Jean-Noël Grad


This release provides a number of corrections for Espresso 4.1.
We recommend that this release be used for all production simulations.
The interface is mostly unchanged between Espresso 4.1 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.
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

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

* 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)

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