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Add 4.1.1 release notes in master #3332

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103 changes: 103 additions & 0 deletions NEWS
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,109 @@
= ESPRESSO NEWS =
=================

ESPResSo 4.1.1
==============

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 https://github.com/espressomd/espresso

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)




Espresso 4.1
============

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