ESPResSo 4.1.3 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 4.1.2 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)