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Jean-Noël Grad edited this page Apr 9, 2021 · 45 revisions

These are the draft release notes for ESPResSo 4.2

ESPResSo 4.2

This is a feature release, i.e., new functionality is added to ESPResSo.

Changed requirements

  • LaTeX is no longer a requirement for building the Sphinx documentation and running the tutorials (#3256, #3395)

  • The minimal versions of all dependencies was increased (#3375, #3687, #3878, #3984, #3994, #4115): Python 3.6, Cython 0.29, CMake 3.16, Boost 1.66, and Python packages based on versions available in Ubuntu 20.04.

  • CUDA 11 support was added (#3870)

  • CUDA 8 and CUDA 9 support was removed (#3984)

  • AMD GPU support via ROCm (HCC and HIP-Clang compilers) was removed (#3966)

  • library libcuda is no longer a dependency in CUDA builds (#4095)

Added functionality and documentation

  • Brownian Dynamics simulations can be carried out with the newly added Brownian integrator and Brownian thermostat (#1842)

  • Stokesian Dynamics simulations can be carried out with the newly added Stokesian integrator and Stokesian thermostat (#3790, #3987)

  • Incompatible thermostat/integrator combinations will now throw an error (#3880)

  • Profile observables now provide methods bin_centers() and bin_edges() to facilitate plotting (#3608)

  • Accumulator and Correlator classes now return the data in suitably shaped multi-dimensional numpy arrays; dependent properties such as lag times and sample sizes need to be obtained separately by calling methods (#3848)

  • Shapes can be merged into meta-shapes (#3493, #3538)

  • A parametric weight function was added to the DPD interaction (#3570)

  • H5MD output files now support a unit system (#3751)

  • MDAnalysis integration now provides bond information (#3801)

  • ScaFaCoS integration now supports activating an electrostatics ScaFaCoS actor at the same time as a magnetostatics ScaFaCoS actor (#4036)

  • MMM1D now throws an error for incorrect periodicity or cell system instead of causing a segfault (#4064)

  • CUDA errors now halt the flow of the program by throwing a Python exception with a clear error message (#4095)

  • The particle director can now be set from the python interface (#4053)

  • The particle method vs_auto_relate_to() can now take a particle as argument instead of a particle id (#4058)

  • Particles can now be serialized and deserialized in the python interface with particle_dict = p.to_dict() and system.part.add(particle_dict) (#4060)

  • The LB grid now supports slicing operations (#4195).

  • The Electrokinetics class now has an extra optional parameter ext_force_density, for consistency with other LB implementations (#4203)

  • Cylindrical observable classes have an extra transform_params argument to change the orientation of the cylindrical coordinates systems and control the origin of the phi angle (#4152)

  • The Reaction Field electrostatic method is now documented (#4218)

  • The user guide chapter on thermostats was moved to the chapter on integrators, since they are tightly coupled (#4080)

  • Tutorials 01, 02, 04 and 05 have been improved (#3408, #3881, #3914, #3893)

  • Tutorials now use the exercise2 plugin to hide solutions (#3872)

  • Tutorials have been re-organized by difficulty level (#3993)

  • Scientific publications referenced in comment lines in the core have been converted to BibTeX citations and moved to doxygen blocks to make them more accessible (#3304)

Feature configuration at compile time

  • GPU support is now opt-in (#3582). Pass the CMake flags -DWITH_CUDA=ON to compile CUDA code and optionally -DWITH_CUDA_COMPILER=<compiler> to select the CUDA compiler: NVCC (default), Clang.

  • Optional features HDF5, ScaFaCoS and Stokesian Dynamics are now opt-in (#3735, #4112). If they are requested with the corresponding -DWITH_<FEATURE>=ON flag and their dependencies are not found, CMake will raise an error. In the original build system, CMake would silently ignore these features if the dependencies were not found, causing confusion as to what was exactly compiled.

  • The LANGEVIN_PER_PARTICLE feature was renamed to THERMOSTAT_PER_PARTICLE (#4057)

Interface changes

  • The NpT thermostat now uses the Philox random number generator and requires a random seed on first instantiation (#3444).

  • The global Mersenne Twister RNG was removed (#3482). All thermostats are now Philox-based. Local Mersenne Twister RNGs are still used in the linear polymer position generator (now with proper warmup) and in the ReactionAlgorithm class.

  • The polymer setup code was moved from the core to Python (#3477). The espressomd.polymer.positions() function was renamed to espressomd.polymer.linear_polymer_positions() and the espressomd.diamond.Diamond class was converted to function espressomd.polymer.setup_diamond_polymer(). For diamond polymers, counter-ions must now be added manually by the user.

  • It is no longer necessary to manually reshape the output of Observable objects. The Observable classes now return multi-dimensional numpy arrays and the documentation clearly indicates the shape and size of the calculated data (#3560). The same applies to Accumulators and TimeSeries (#3578)

  • The observable ComForce was renamed to TotalForce, to reflect in the name what it actually calculates (#3471).

  • The RDF feature was removed from the Analysis module and converted to an Observable class (#3706). Time averages can be obtained using the TimeSeries accumulator.

  • All occurrences of "Stress Tensor" in the Analysis module and LB module were renamed to "Pressure Tensor" to better reflect what is actually calculated (#3723)

  • The MeanVarianceCalculator interface was changed (#3996)

  • Observable parameters are now immutable (#4206, #4211)

  • The system.cuda_init_handle.list_devices() feature is now a function, and the system.cuda_init_handle.list_devices_properties() function disabled in 4.0.0 was restored (#4095)

  • Parameter particle_scales of coupling-based fields PotentialField and ForceField now takes a dict object instead of a list of tuples (#4121)

  • Several parameters of the ICC class are no longer optional: epsilons, normals, areas, sigmas (#4162)

  • The ELC actor is no longer an electrostatics extension (#4125). The ELC actor now takes a P3M actor as argument and modifies it. Only the ELC actor needs to be added to the system list of actors. The ELC actor can be removed from the list of actors.

Changed and removed functionality

  • The active matter tutorial was converted into a Jupyter notebook (#3395)

  • The reaction ensemble tutorial deprecated in 4.1.1 was removed (#3256)

  • The PdbParser feature deprecated in 4.1.1 was removed (#3257)

  • The ENGINE shear torque calculation feature deprecated in 4.1.1 was removed (#3277)

  • The MEMBRANE_COLLISION and OifOutDirection features were removed (#3418)

  • The AFFINITY feature was removed (#3225)

  • The unused and untested UMBRELLA feature was removed (#4032, #4079)

  • The unused and untested VIRTUAL_SITES_COM feature was removed (#3250)

  • The unused and untested EK_DOUBLE_PREC feature was removed (#4192)

  • The unused and untested MD Metadynamics feature was removed (#3563)

  • The unused and untested Stomatocyte shape was removed (#3730)

  • The incorrectly implemented and untested HarmonicDumbbellBond interaction was removed (#3974, #4079)

  • The per-particle temperature feature was removed (#4057)

  • The Current observable was removed in favor of the FluxDensityProfile observable (#3973)

  • The incorrectly implemented analysis function cylindrical_average was removed in favor of the CylindricalDensityProfile observable (#3470)

  • The minimize_energy member of the System class was removed (#3390, #3891). The steepest descent algorithm is now a regular integrator that is set up via the system.integrator.set_steepest_descent() method.

  • The MMM2D electrostatics feature was removed (#3340). Electrostatics in slab geometries can still be achieved by ELC, with significantly better performance.

  • The layered cell system was removed (#3512)

  • The Analysis module min_dist2() function was removed and the dist_to() function was merged into system.distance_vec() (#3586)

  • The Analysis module energy() function now returns the lower triangle of the non-bonded interaction matrix, to be consistent with pressure() and stress_tensor() (#3712)

  • The number of cells for the link cell algorithm can no longer be constrained to a range of values (#3701)

  • The system.cell_system.get_pairs_() method was renamed and now supports filtering particle pairs by type (#4035)

  • The NpT integrator can no longer be used with the GPU implementation of P3M due to the undefined P3MGPU contribution to the virial (#4026)

Improved testing

  • The C++ core of ESPResSo is now 95% covered by unit tests and integration tests.

  • The structure factor code is now tested against simple lattices (#4205)

  • The MMM1D GPU code is now tested (#4064)

  • The Reaction Ensemble core classes are now unit tested (#4164)

Performance enhancements

Bug fixes

  • The transform_vector_cartesian_to_cylinder() now calculates the correct phi angle (#4094). The bug was present since ESPResSo 4.0.0 and affected observables CylindricalVelocityProfile, CylindricalFluxDensityProfile, CylindricalLBVelocityProfile, CylindricalLBVelocityProfileAtParticlePositions, CylindricalLBFluxDensityProfileAtParticlePositions.

  • Several memory leaks were fixed in the TabulatedBond interactions (#3961), electrostatics and magnetostatics tuning functions (#4069), and LB feature (#4108)

  • The system.actors.clear() method was broken and would only remove half of the actors since 4.0.0. This is now fixed (#4037).

  • Adding a LB thermostat when any other thermostat was already active would silently fail since 4.0.0. This is now fixed (#4116).

  • Setting the NpT or steepest descent integrators with incorrect parameters no longer leaves the system in an undefined state (#4026).

  • The OpenGL visualizer had a tendency to slow down after pausing and resuming the simulation, or freezing when using the steepest descent integrator. This was due to a race condition between two threads that has been fixed (#4040).

  • It is no longer possible to accidentally set a non-cubic NpT integrator with P3M (#4165)

  • Illegal LB node access is now properly caught by exceptions (#3978)

  • Accessing the flux property of EK species no longer throws an error (#4106)

  • The LB grid in the GPU implementation is now automatically resized when the simulation box size changes (#4191)

  • The ELC and MDLC actors now throw an error when a particle enters the gap region (#4051)

  • The dipolar direct sum with replica method is now disabled on periodic systems with zero replica, as it does not apply minimum image convention (#4061)

  • The DipolarP3M checkpointing mechanism was fixed (#3879)

  • P3M-based actors now sanitize the user-provided alpha and accuracy parameters and no longer allow constraining the alpha parameter during tuning (alpha was always derived from the other parameters at the end of tuning) (#4118)

  • The Debye-Hückel range check now accepts a prefactor of 0 for consistency with other electrostatic methods (#4218)

  • A buffer overflow in the DipolarP3M tuning function lead to random failures during tuning, this is now fixed (#3879)

  • A buffer overflow in the LB code could lead to incorrect results in grids of size 9x9x9 or larger with open boundaries, this is now fixed (#4078)

  • The EK feature now generates VTK files that are compliant with the VTK 2.0 standard (#4106)

  • It is no longer possible to accidentally add the same bond twice on the same particles (#4058)

  • Providing incorrect parameters to the ScaFaCoS actors no longer cause ESPResSo to crash (#4068)

  • Constant parameters default_scale, particle_scales and gamma of coupling-based fields PotentialField, ForceField, FlowField and HomogeneousFlowField now throw an error when an attempt is made to change their value via the class setter, instead of silently ignoring the new value (#4121)

  • The observable CylindricalLBFluxDensityProfileAtParticlePositions now measures the correct quantity (#4152)

  • Providing incorrect values to the histogram ranges in profile-based observables (e.g. min_x > max_x) now throws an error (#4211)

  • The Boost 1.74 bug was patched (#3978)

  • A bug involving an access out of bounds was fixed in the structure factor code (#4205)

New tutorials

Under the hood changes

  • The Python code is now checked with Pylint to prevent the introduction of unused code and dangerous anti-patterns (#3293, #3203)

  • The Python code and C++ code are now checked with LGTM to detect coding errors and anti-patterns (#3851, #3856)

  • The CMakeLists.txt files are now formatted automatically with cmake-format (#3622)

  • The Particle struct was moved to a dedicated header file Particle.hpp to improve separation of concerns in the core (#3251, #3164).

  • The Observable_stat structs were moved to a dedicated header file Observable_stat.hpp and decoupled from the pressure/energy/coulomb/dipolar frameworks (#3712) and made stateless (#3723)

  • Observables based on particle ids have been rewritten using particle traits to decouple the Particle struct from Observable classes (#3667)

  • The Python Integrator class was split in multiple classes, one for each integrator, with a structure similar to actor and interaction classes (#3390). This layout better reflects the structure of integrators in the core and will make it easier to include new integrators in the future. This change doesn't break the API.

  • The ghost communication infrastructure was simplified (#3216, #3399)

  • Thermostats are now fully object-oriented in the core to reduce code duplication (#3438, #3444, #3461)

  • Bonded interactions are now fully object-oriented in the core to facilitate the development of new interactions (#4161)

  • The local_particles global variable is no longer accessible directly (#3501)

  • The Python tests now use specialized assertions to generate more helpful error messages (#3419)

  • The tutorial tests were simplified using AST to parse Jupyter notebooks (#3408)

  • The CMake logic for tutorials has been simplified (#3408, #3486)

  • The Cython interface was thoroughly cleaned up from unused imports (#3496, #3510)

  • The ScriptInterface backend was rewritten (#3794)

  • The duplicated functions between P3M and DipolarP3M were factored out (#3879)

  • Statistical tests are no longer executed in coverage and sanitizers builds (#3999)

  • The Utils::Mpi::gather_buffer() function was fixed (#4075). The bug didn't affect ESPResSo.

  • Clang 10 warnings were addressed (#4084)

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