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Jean-Noël Grad edited this page Mar 4, 2022 · 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

  • The minimal version of all dependencies was increased (#3375, #3687, #3878, #3984, #3994, #4115, #4312, #4337): Python 3.7, Cython 0.29.14, CMake 3.16, Boost 1.69, Sphinx 2.3.0 and Python packages based on versions available in Ubuntu 20.04.

  • CMake no longer emits a warning about the deprecated distutils Python package, which is no longer a requirement (#4433)

  • 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)

  • Installation instructions for ESPResSo on Microsoft Windows via WSL are now available (#4348)

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

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)

  • Lees-Edwards boundary conditions can be used for particle-based simulations (#4457). Lattice-Boltzmann support will be added in release 4.3.0.

  • Bonded interactions can now be automatically broken when the bond length exceeds a critical value (#4456). This feature can be combined with collision detection to model reversible bonds (#4464).

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

  • 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) and checks if the MDAnalysis package version is supported (#4386)

  • 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) and LB slices are equality comparable (#4268).

  • 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 Lennard-Jones, 02 electrostatics, 04 lattice-Boltzmann and 05 raspberry electrophoresis have been improved (#3408, #3881, #3914, #3893, #4302)

  • Tutorial 04 lattice-Boltzmann was split into three tutorials: polymer diffusion, Brownian motion and Poiseuille flow (#4052, #4329)

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

  • Tutorials have been renamed and organized by difficulty level (#3993)

  • The OpenGL visualizer now offers control over the radius of LB velocity arrows, documents all LB-related keyword arguments, and fixed a division-by-zero that triggered a runtime warning for fluid inside boundaries (#4376)

  • A Gibbs ensemble sample was added to simulate the exchange of particles between two ESPResSo systems via the multiprocessing Python module (#4243)

  • The user guide now includes a button on python code samples to hide terminal output and Python prompt symbols (>>> and ...), so as to facilitate copy-pasting examples directly in the terminal and in user scripts (#4386).

  • 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.

  • Experimental support for fast-math mode was added (#4318). Some features might break depending on the compiler used to build ESPResSo. Please quantify the numerical stability of your simulations before enabling fast-math mode in production.

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

  • The magnetostatic extension DLC now depends on feature DIPOLES instead of DP3M, since FFTW is not a dependency of DLC (#4238)

  • The electrostatic extension ICC now depends on feature ELECTROSTATICS instead of P3M, since FFTW is not a dependency of ICC (#4238)

  • The MMM1D_MACHINE_PREC feature was added to enable Chebychev series for MMM1D on CPU without the need to define the (now removed) BESSEL_MACHINE_PREC macro (#4311)

Interface changes

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

  • 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, LB module and EK module were renamed to "Pressure Tensor" to better reflect what is actually calculated (#3723, #4228)

  • 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)

  • The MeanVarianceCalculator interface was changed (#3996)

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

  • Bonds are now immutable (#4350). Bonds added to the list of bonds can no longer be overwritten by a bond of a different type, as it could lead to undefined behavior when the number of bonded partners was higher in the overwriting bond. Bonds can now be removed from the list of bonds, after they have been removed from particles.

  • 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)

  • The System class no longer has a global member (#4276). Global variables are still accessible from other members of the System class.

  • Cluster analysis class Cluster no longer returns False when a string passed to call_method() doesn't match the name of a core method; instead None is returned (#4234)

  • Cluster analysis class ClusterStructure no longer returns True when the corresponding core method doesn't return a value; instead None is returned (#4234)

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

  • Electrostatic and magnetostatic methods that support tuning now have a timings argument to control the number of integration loops to run during tuning (#4276)

  • 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 now be removed from the list of actors.

  • The Drude helpers (global variables and free functions) have been gathered into a checkpointable class DrudeHelpers, which now relies on particle handles instead of particle ids (#4353)

  • Observables now check their input parameters (#4211, #4255) and raise a Python exception when an invalid value is detected (e.g. min_x > max_x in profile-based observables)

  • The argument temperature in reaction methods was renamed to kT for clarity (#4305)

  • All reaction methods now take keyword arguments instead of positional arguments (#4451)

  • Reaction method constraints can now be changed from cylindrical to slab safely and can be removed (#4310). They will also raise an error when created with invalid parameters.

  • The MPI-IO feature now raises an exception from which the user can recover when the simulation script runs on 1 MPI rank, instead of an unrecoverable fatal error (#4455). This change is meant to help debugging read/write errors in simulation scripts. On 2 or more MPI ranks, exceptions still lead to a fatal error.

  • The []-operator on system.part was removed (#4402). Use system.part.by_id(1) to fetch a specific particle, system.part.by_id([1, 3]) to fetch a group of particles, or system.part.all() to fetch all particles. This change was necessary to resolve the ambiguity of particle slices containing non-contiguous particle ids.

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 unused Wang-Landau reaction ensemble algorithm was removed (#4288)

  • 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 domain decomposition cell system was renamed to regular decomposition (#4442)

  • 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)

  • 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 constant pH method now implements a symmetric proposal probability instead of an asymmetric proposal probability (#4207)

  • It is no longer possible to checkpoint an ESPResSo system instance that contains LB boundaries, constraints or auto-update accumulators, when the simulation is running with 2 or more MPI nodes. An error will be raised (#4287).

  • It is no longer possible to checkpoint an Electrokinetics instance, and its parameters are now immutable (#4327).

  • Th LBBoundaries slip velocity check was lowered to Mach 0.35, or 0.2 in LB units (#4376)

  • The WidomInsertion.measure_excess_chemical_potential() method was replaced by WidomInsertion.calculate_particle_insertion_potential_energy(), which returns the instantaneous value of the excess chemical potential instead of the accumulated mean and standard error (#4374). The mean value and standard error of the excess chemical potential must be now be calculated in WidomInsertion.calculate_excess_chemical_potential().

  • The mpiio global variable was removed (#4455). The MPI-IO feature can still be used by creating a local instance with mpiio = espressomd.io.mpiio.Mpiio().

Improved testing

  • The C++ core of ESPResSo is now 97% covered by unit tests and integration tests (#4426).

  • 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

  • The ReactionAlgorithm::do_reaction() function used by reaction methods now caches the potential energy of the system and only updates it after a successful reaction trial move (#4374).

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), lattice-Boltzmann code (#4108) and Barnes-Hut code (#4404)

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

  • The ClusterStructure feature did not properly handle box periodicity since 4.0.0 and would under rare circumstances calculate a center of mass to be outside a fully periodic simulation, and would incorrectly fold coordinates in aperiodic systems. This is now fixed (#4363).

  • 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)

  • EK node access now requires integer values for node indices (#4228)

  • 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 lattice-Boltzmann python interface no longer ignores runtime errors, nor converts them to cryptic system errors (#4355).

  • The script interface no longer silently ignores runtime errors when converting python objects to C++ data types (#4387).

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

  • The ELC actor is now updated when the box size changes in the z-direction (#4231)

  • The DLC actor no longer crashes the system when tuning fails, instead a Python exception is raised (#4238)

  • 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)

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

  • Virtual sites now contribute to the rotational kinetic energy of the system (#4198)

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

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

  • The Boost 1.74 bug was patched (#3978)

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

  • Passing a particle chain-based observable object (ParticleDistances, BondAngles, BondDihedrals, CosPersistenceAngles) that doesn't have enough particle ids for the calculation (e.g. only 1 particle id when 2 are needed for the bond distance calculation) to a Correlator object no longer causes a memory overflow (#4255).

  • Calculating the energy of the system when an IBM object is present no longer terminates ESPResSo, instead a warning is issued (#4286).

  • The Sphere shape no longer returns NaN values in the distance vector for particles located exactly at its center (#4384).

  • Runtime errors raised when the maximal bonded interaction range becomes larger than the simulation box are no longer ignored when dihedral bonds are added to the list of interactions (#4383).

  • Runtime errors about incorrectly initialized electrostatic and magnetostatic methods are no longer silently ignored at the integration start (#4383).

  • Runtime errors about incorrectly initialized GPU dipolar direct sum and Barnes-Hut are no longer silently ignored when the actors are instantiated (#4404)

  • Compiler warnings from Clang 13.0.0 and GCC 12.0.0 were addressed (#4426)

New tutorials

  • The active matter tutorial was completely rewritten and is now interactive (#4304)

  • An error analysis tutorial was added (#4174)

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)

  • Bonded interactions are now communicated between MPI processes automatically and transparently by the script interface (#4350)

  • The MPI callback code in the core has been simplified and made more homogeneous (#4383)

  • 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 framework was rewritten (#3794)

  • The ScriptInterface framework is now the preferred way to implement new features. Existing features were converted to ScriptInterface objects: bonded interactions (#4350), bond breakage (#4464), reaction methods (#4451), MPI-IO (#4455)

  • 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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