Espresso 4.1.3 released

[Jean-Noël Grad]

Dear Espresso users,

The Espresso team is pleased to announce the release of Espresso 4.1.3. 
The source can be downloaded at 
https://github.com/espressomd/espresso/releases/download/4.1.3/espresso-4.1.3.tar.gz
Please see the release notes below.


Many thanks to all contributors!
Regards,
Jean-Noël Grad

============

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 4.1.2 and 4.1.3.
However, some bugs were discovered which can affect simulation results.
Please find the list of changes below. The numbers in brackets refer to
ticket numbers on https://github.com/espressomd/espresso

Feature configuration at compile time

* The number of features which need to be defined at compile time in
  myconfig.hpp has been reduced. Features without performance impact
  are now always present. These are:

   * ``OIF_LOCAL_FORCES``
   * ``OIF_GLOBAL_FORCES``

General corrections and improvements:

* Many bonded interactions were not considered in the bond cutoff
  calculation: umbrella, OIF local, OIF global, IBM tribend, IBM
  volcons, angle harmonic, angle cosine, angle cossquare, tabulated
  angle, bonded Coulomb, subtracted bonded Coulomb, subtracted LJ,
  quartic, harmonic dumbbell. This can lead to sub-optimal skin values
  when such bonds are used with an inter-particle distance that is
  longer than other bonded (FENE, harmonic bond, rigid bond,
  thermalized distance, tabulated bond, tabulated dihedral, dihedral,
  IBM triel), non-bonded (LJ, Morse, Buckingham, etc.) and long-range
  (electrostatics, magnetostatics) interactions in the same system. All
  bonded interactions are now considered in the cutoff calculation
  (#3443).

* Fix a bug in a rotation function that resulted in improper treatment
  of rotation vectors with norm different from unity (#3559); all
  observable classes inheriting from `CylindricalProfile` are affected

* Fix a bug in the LB GPU implementation that lead to incorrect velocity
  interpolation near LB boundaries (#3593)

* Fix a bug in the LB CPU implementation that lead to incorrect grid
  sizes (#3678)

* Object-in-fluid bugfixes have been backported from the OIF development
  branch; in particular, the bending force between two triangles is now
  torque-free (#3385)

* Rewrite the linear polymer position generator, which was inefficient
  and frequently rejected valid positions (#3402, #3484, #3491)

* Fix an error in the distance calculation of the `SpheroCylinder`
  shape (#3629)

* Fix a sign flip in the surface normal calculation of the `Torus`
  shape (#3728)

* Fix an `IndexError` when running `system.number_of_particles()`
  without a value for the argument `type` (#3496, #3494) and fix the
  range check (#3536)

* Fix a `NameError` when running `system.analysis.rdf()` without a value
  for the argument `r_max` (#3496, #3494)

* Fix a `NameError` raised by the OpenGL visualizer when drawing bonds
  in periodic images of the unit cell (#3511)

* Correctly calculate the orientation of bonds cut by the faces of the
  simulation box in the OpenGL visualizer (#3511)

* Fix a memory leak in the OpenGL visualizer when drawing shapes
  containing cylindrical elements (`Cylinder`, `SpheroCylinder`,
  `SimplePore`, `Slitpore`) and drawing bonds between particles (#3533)

* Fix an issue in the OpenGL visualizer that drew the channel of the
  `Slitpore` shape at the center of the box, instead of using the
  `dividing_plane` attribute (#3728)

* Fix a bug in the ELC algorithm that ignored the Coulomb prefactor
  (#3731). The same bug is also present in MMM2D but could not be fixed.

* Correctly check the P3M parameter `mesh` (#3676)

* The LB checkpointing argument `binary` now takes a boolean value
  (#3541); integers values 0 and 1 are still accepted (integers are
  implicitly cast to boolean values)

* Reinitialize the P3M and dipolar P3M solvers when the box size or skin
  changes (#3717)

* Clarify error messages in the Steepest Descent integrator (#3763)

* Fix an incorrect formula in the `tensor_product` mode of the
  `Correlator` class that always returned an array of 0's since 4.1.0
  (#3781)

* Fix a runtime error when calling the `get_params()` method of a
  ScaFaCoS-based actor (#3784)

Documentation and tutorials corrections and improvements:

* Fix paragraph formatting in Jupyter notebooks and update Sphinx
  bibliography (#3395).

* The Sphinx documentation generation doesn't run in parallel any longer
  due to plugin `sphinxcontrib.bibtex` throwing a warning when executed
  with more than one thread in Sphinx v2.3.1 (#3393). The slowdown is
  not significant (less than a second).

* Fix compatibility issues with Sphinx 2.4.0 (#3480), 3.0.1 (#3642,
  #3659) and 1.6.7 (#3743)

* Clarify the quaternion formalism used in ESPResSo (#3392, #3748)

* The `p3m.py` sample showcased an incorrect usage of the ELC actor
  (the gap region was missing). The actor was removed and a new,
  stand-alone sample `visualization_elc.py` was created (#3468)

* The `visualization_constraints.py` sample showcased an incorrect
  usage of the `Slitpore` and `Wall` shapes that lead to a discontinuous
  potential; this is now fixed (#3728)

* Correct errors in the documentation of the constructor parameters for
  shape classes `Cylinder`, `SpheroCylinder`, `Rhomboid` (#3567), for
  class `System` (#3542) and for cylindrical observables (#3569)

* Correct an error in the formula of the electrostatic prefactor in the
  electrostatics documentation, give the full expression of the
  electrostatic prefactor in tutorials and samples (#3673)

* Improve documentation of the `Slitpore` shape and document the
  `Torus` shape (#3728)

* Improve installation instructions (#3673, #3699, #3732)

* Document `BoxGeometry`-related functions (#3747)

* Explain release workflow and how to obtain released versions of
  ESPResSo (#3745)

* Improve citation instructions with examples (#3745)

* General improvements (#3740, #3743)

Build system and platform-related corrections and improvements:

* The benchmarks can now be run with any MPI library supported by
  ESPResSo (#3412)

* The CMake logic was simplified (#3574, parts of #3582). The minimal
  required Cython version is now checked. CMake now generates an error
  message if `WITH_CLANG_TIDY` is `ON` but no Clang-Tidy can be found
  with a version matching the Clang version. The CUDA library installed
  via the Ubuntu package `nvidia-cuda-toolkit` is now correctly
  detected.

* Add support for ROCm versions 3.0 (#3386), 3.1 (#3574) and 3.3 (#3623)

* Fix compiler errors with HDF5 > 1.10.2 (#3604)

* Fix compiler errors with Boost 1.73 (#3725)

* Fix a deprecation warning from the `collections.abc` that will become
  an error in the upcoming Python 3.9 interpreter (#3568)

* Fix a compatibility issue with `pint` 0.10.1 in tutorial
  12 - constant pH (#3423)

Improved testing:

* Fix a tolerance value that was incorrectly divided by 100, causing
  unit tests to fail on i586 architectures (#3427)

* Compile CUDA code in the Travis-CI image to detect more compiler
  errors (#3699). GPU tests are skipped on Travis-CI.

* Add a test for the ``Utils::get_n_triangle`` function used in OIF
  (#3391)

* Add a test for sample `visualization_constraints.py` (#3533)

* Add missing `LENNARD_JONES` and `GPU` feature guards in Python
  tests (#3403, #3676)

* Fix a few non-functional Python tests (#3419) and sample tests (#3791)

* Improve testing of ELC (#3731)

* Improve testing of the `Slitpore` shape (#3728)

* Fix an issue in a core test (#3677)

* Add cleanup function in the checkpointing tests (#3699)

* Add a test for `fold_position()` (#3747)

* Improve testing of observables, correlators and accumulators
  (#3781, #3783, #3784)

Under the hood changes:

* Remove unused code (#3556, #3738)

* Remove the unused `FindPythonModule` CMake module (#3736)

* Update the espresso-ci bot scripts (#3613)