Category: News

Invitation to the ESPResSo Summer School 2022

Simulating the dynamics of soft matter with ESPResSo, PyStencils and LbmPy

Date:
October 10, 2022 – October 14, 2022

Location:
hybrid format: onsite course at the ICP, University of Stuttgart (Germany) with live streaming on Zoom for online participants

Register:
https://www.cecam.org/workshop-detail/1146

Schedule: PDF

Notes from the Organizers

This school is currently planned as an onsite event. If the Covid-rules applicable in autumn do not allow it, we will adjust the format of the school to allow remote attendance.

Course description

In this school, students learn to conduct simulations in the fields of statistical physics, soft matter and active matter using the software ESPResSo. It is an open-source particle-based simulation package with a focus on coarse-grained molecular dynamics models. In addition, it offers a wide range of schemes for solving electrostatics, magnetostatics, hydrodynamics and electrokinetics, as well as algorithms for active matter and chemical reactions[1].

ESPResSo consists of an MPI-parallelized simulation core written in C++ and a scripting interface in Python which integrates well with science and visualization Python packages, such as numpy and PyOpenGL. ESPResSo relies on waLBerla, a high performance lattice-Boltzmann library, for hydrodynamics and other lattice-based schemes for electrokinetics and related fields[2].

In this school, after an introduction to particle-based simulations and the software interface, we will focus on the dynamics of soft matter. We will explore topics such as electrophoretic mobility of colloids, diffusion of polymers, and studying rheology using Lees-Edwards boundary conditions. In addition to particle-based approaches, we will cover the lattice-Boltzmann method for hydrodynamic interactions and a diffusion-advection-reaction solver for modelling electrokinetics and catalysis.  Lectures will provide an introduction to the physics and simulation model building as well as an overview of the necessary simulation algorithms. During the afternoon, students will practice running their own simulations in hands-on sessions.

Many of the lectures and hands-on sessions will be taught by developers of the software. Hence, the school will also provide a platform for discussion between developers and users about the future of the software. Moreover, users can get advice on their specific simulation projects. Time will also be dedicated to research talks, which illustrate how the simulation software is applied, and which provide further background in the field of soft matter dynamics.

Attendance to the summer school is free.

[1] F. Weik, R. Weeber, K. Szuttor, K. Breitsprecher, J. de Graaf, M. Kuron, J. Landsgesell, H. Menke, D. Sean, C. Holm, Eur. Phys. J. Spec. Top., 227, 1789-1816 (2019) DOI:10.1140/epjst/e2019-800186-9
[2] M. Bauer, S. Eibl, C. Godenschwager, N. Kohl, M. Kuron, C. Rettinger, F. Schornbaum, C. Schwarzmeier, D. Thönnes, H. Köstler, U. Rüde, Computers & Mathematics with Applications, 81, 478-501 (2021) DOI:10.1016/j.camwa.2020.01.007
[3] M. Bauer, J. Hötzer, D. Ernst, J. Hammer, M. Seiz, H. Hierl, J. Hönig, H. Köstler, G. Wellein, B. Nestler, U. Rüde, Code generation for massively parallel phase-field simulations. Published in: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (2019) DOI:10.1145/3295500.3356186

ESPResSo 4.2.0 released

This is a feature release, i.e., new functionality is added to ESPResSo. New thermostats, cell systems and boundary conditions have been introduced to simulate systems with Stokesian Dynamics, Brownian Dynamics, strongly inhomogeneous particle sizes or translation-invariant shear flow. The interface underwent (non-silent) changes, therefore scripts will have to be slightly adapted. Most notably, particle access by id and particle slices have a new syntax, and electrostatic/magnetostatic layer correction and reaction methods have a different setup. All errors are also now emitted as Python exceptions and are recoverable with minimal effort.

An additional focus of this release is the simplification of both the C++ core and the Python script interface to facilitate future extensions of ESPResSo. The testing of ESPResSo’s functionality has been extended considerably.

We recommend that this release be used for all production simulations. No further bug fix releases will be provided for the 4.1 line, and not all fixes are present in ESPResSo 4.1.4.

Please carefully read the detailed list of changes below before using this release. Issues can be reported at https://github.com/espressomd/espresso.

Get the source code in the Download area.

Added functionality

  • P3MGPU now supports energy and pressure calculation via the CPU kernels (#4506).
  • ELC now works with P3MGPU (#4506).
  • The LB grid now supports slicing operations (#4195) and LB slices are equality comparable (#4268).
  • Lees-Edwards boundary conditions can be used for particle-based simulations (#4457). Lattice-Boltzmann support will be added in the 4.3.0 release.
  • The non-bonded energy of a single particle can be calculated (#4401).
  • The list of close neighbors of a single particle can be extracted (#4401).
  • 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).
  • 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).
  • A new cell system HybridDecomposition was introduced to speed up simulations with inhomogeneous particle interaction ranges (#4373).
  • Shapes can be merged into meta-shapes (#3493, #3538).
  • The HollowConicalFrustum can now be sliced open, made thick and rotated to model quarter pipes in any orientation (#4179). The main application is in the construction of complex microchannel geometries via LBBoundaries.
  • A parametric weight function was added to the DPD interaction (#3570).
  • H5MD output files now support a unit system (#3751).
  • H5MD output files now support custom specifications to control which particle and box properties to write to disk (#4480).
  • The H5md class is now checkpointable and usable in an interactive Python session (#3751).
  • MDAnalysis integration now provides bond information (#3801).

Changed requirements

  • The minimal version of all dependencies was increased (#3375, #3687, #3878, #3984, #3994, #4115, #4312, #4337, #4489): Python 3.8, Cython 0.29.14, CMake 3.16, Boost 1.69, Sphinx 2.3.0, and Python packages versions are pinned on versions available in the Ubuntu 20.04 repository.
  • CMake no longer emits a warning about the deprecated distutils Python package, which is also 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).

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 their -DWITH_<FEATURE>=ON flag and their dependencies are not found, CMake will raise an error. In the older 4.1 build system, CMake would silently ignore these features when their 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).
  • The EXPERIMENTAL_FEATURES feature was removed (#4482).

Improved documentation

  • Tutorials have been renamed and organized by difficulty level (#3993).
  • Tutorials Lennard-Jones, electrostatics, lattice-Boltzmann, raspberry electrophoresis and constant-pH have been improved (#3408, #3881, #3914, #3893, #4302, #4262).
  • Tutorial lattice-Boltzmann was split into three tutorials: polymer diffusion, Brownian motion and Poiseuille flow (#4052, #4329).
  • The active matter tutorial was rewritten into a Jupyter notebook (#3395, #4304).
  • An error analysis tutorial was added (#4174).
  • Tutorials now use the exercise2 plugin to hide solutions (#3872); since this plugin only exists for the classic Jupyter Notebook, a conversion script is provided for JupyterLab users (#4522).
  • 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 (#4386).
  • The user guide now uses a responsive theme for mobile/tablet users (#4504).
  • The user guide chapter on thermostats was moved to the chapter on integrators, since they are tightly coupled (#4080).
  • Mentions to non-existent functions were removed from the user guide (#4482).
  • Scientific publications referenced in comment lines in the core have been converted to BibTeX citations and integrated into Doxygen blocks to make them accessible in the Doxygen HTML documentation (#3304).
  • The Reaction Field electrostatic method is now documented (#4218).
  • The H5MD feature is now better documented (#4480).
  • A Gibbs ensemble sample was added to simulate the exchange of particles between two ESPResSo systems via the multiprocessing Python module (#4243).
  • A reaction ensemble sample was added to simulate a complex chemical reaction involving 5 chemical species (#3778).

Interface changes

  • The system.set_random_state_PRNG() method was removed (#3482).
  • 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.
  • The domain decomposition cell system was renamed to regular decomposition (#4442). The system.cell_system.set_domain_decomposition() function was renamed to system.cell_system.set_regular_decomposition().
  • 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.
  • Observable parameters are now immutable (#4206, #4211).
  • The Electrokinetics actor parameters are now immutable (#4327).
  • The LBFluid, LBFluidGPU, Electrokinetics and Species methods print_*() have been renamed to write_*() (#4049).
  • The ELC actor is no longer an electrostatics extension (#4125, #4506). The ELC actor now takes a P3M or a P3MGPU 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 DLC actor is no longer a magnetostatic extension (#4506). The DLC actor now takes a magnetostatic actor as argument and modifies it. Only the DLC actor needs to be added to the system list of actors.
  • The NpT thermostat now uses the Philox random number generator and requires a random seed on first instantiation (#3444).
  • 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 analysis module energy(), pressure() and pressure_tensor() functions now return only two slots for electrostatics and magnetostatics: short-range contribution in the first slot and long-range contribution + layer correction in the second slot (#3770).
  • The analysis module pressure() and pressure_tensor() functions no longer provide a velocity-compensation flag to compute the pressure at half the time step in NpT simulations (#3756).
  • The espressomd.reaction_ensemble module was renamed to espressomd.reaction_methods (#4482).
  • 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).
  • The constant pH method now implements a symmetric proposal probability instead of an asymmetric proposal probability (#4207).
  • The reaction method parameter exclusion_radius was renamed to exclusion_range (#4469).
  • Reaction method now take an optional parameter exclusion_radius_per_type for better control of the exclusion radius in simulations involving different particle sizes (#4469).
  • 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 by WidomInsertion.calculate_excess_chemical_potential().
  • Reaction method constraints can now be safely changed from cylindrical to slab and can be removed (#4310). They will also raise an error when created with invalid parameters.
  • The mpiio global variable was removed (#4455). The MPI-IO feature is now used by creating a local instance with mpiio = espressomd.io.mpiio.Mpiio().
  • 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 H5md class takes new arguments during instantiation (#3785).
  • The system.cell_system.get_pairs_() method was renamed to system.cell_system.get_pairs() and now supports filtering particle pairs by type (#4035).
  • 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.
  • The particle director can be set from the Python interface (#4053).
  • The particle method vs_auto_relate_to() can take a particle as argument instead of a particle id (#4058).
  • Particles can be serialized and deserialized in the Python interface with particle_dict = p.to_dict() and system.part.add(particle_dict) (#4060).
  • 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 time series (#3578).
  • 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 lag_times() resp. sample_sizes() (#3848).
  • Profile observables provide methods bin_centers() and bin_edges() to facilitate plotting (#3608).
  • The observable ComForce was renamed to TotalForce, so as to better reflect 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).
  • The MeanVarianceCalculator interface changed (#3996).
  • Observables now check their input parameters (#4211, #4255) and raise an exception when an invalid value is detected (e.g. min_x > max_x in profile-based observables).
  • 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).
  • Incompatible thermostat/integrator combinations raise an exception (#3880).
  • 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).
  • CUDA errors now halt the flow of the program by throwing a Python exception with a clear error message (#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 globals member (#4276). Global variables are still accessible from other members of the System class.
  • Methods from the 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).
  • Methods from the cluster analysis class ClusterStructure, integrator classes and interaction classes no longer returns True when the corresponding core method doesn’t return a value; instead None is returned (#4234, #4516).
  • Several parameters of the ICC class are no longer optional: epsilons, normals, areas, sigmas (#4162).
  • The electrostatic actors charge neutrality check tolerance can be modified via actor.charge_neutrality_tolerance; this is mostly relevant to actors coupled to ICC, whose induced charges can have values spanning several orders of magnitude (#4506).
  • 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 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).
  • ScaFaCoS integration now supports activating an electrostatics ScaFaCoS actor at the same time as a magnetostatics ScaFaCoS actor (#4036).
  • The list of actors can no longer end up in an invalid state: updating an electrostatic or magnetostatic actor with an invalid parameter now automatically restores the original parameter; inserting an invalid electrostatic or magnetostatic actor in the list of actors now automatically removes the actor from the list of active actors, even when the exception happens during tuning (#4506).
  • The LBBoundaries slip velocity check was lowered to Mach 0.35, or 0.2 in LB units (#4376).
  • The OpenGL visualizer allows changing the radius of LB velocity arrows, documents all LB-related keyword arguments, and no longer suffers from a division-by-zero error that used to trigger a runtime warning for fluid inside boundaries (#4376).
  • The Electrokinetics class got an optional ext_force_density parameter for consistency with other LB implementations (#4203).
  • MDAnalysis integration now checks if the MDAnalysis package version is supported (#4386).

Removed functionality

  • 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 PdbParser feature deprecated in 4.1.1 was removed (#3257).
  • The incorrectly implemented and untested HarmonicDumbbellBond interaction was removed (#3974, #4079).
  • The layered cell system was removed (#3512).
  • The unused Wang-Landau reaction ensemble algorithm was removed (#4288).
  • The reaction ensemble tutorial deprecated in 4.1.1 was removed (#3256).
  • 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 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 analysis module min_dist2() function was removed and the dist_to() function was merged into system.distance_vec() (#3586).
  • The analysis module nbhood() function slab search mode was removed (#4516) since it was incorrect (all ESPResSo versions were affected).
  • The number of cells for the link cell algorithm can no longer be constrained to a range of values (#3701).
  • 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.
  • It is no longer possible to checkpoint an ESPResSo system instance that contains Union shape-based constraints when the simulation is running with 2 or more MPI ranks. An error will be raised (#4287, #4510).
  • It is no longer possible to checkpoint an Electrokinetics instance (#4327).
  • The unmaintained lj-demo.py sample was removed (#4482).
  • The unmaintained mayaviLive visualizer was removed (#4515).

Improved testing

  • The C++ core of ESPResSo is covered by unit tests and integration tests at 98% coverage (#4426, #4479, #4489).
  • The structure factor code is tested against simple lattices (#4205).
  • The MMM1D GPU code is tested (#4064).
  • The reaction method core classes are unit tested (#4164).

Performance enhancements

  • The Particle memory footprint was reduced and the MPI serialization code was improved (#4414). The structure size is now 584 bytes instead of 640 bytes on maxset configuration (10% reduction). All substructures in Particle are bitwise serializable and dynamic vectors are compact vectors. The performance gain is about 9% for a LJ liquid on both maxset and empty configurations, for both 1 000 and 10 000 particles per core.
  • Particle creation happens in constant time instead instead of monotonically increasing with the number of particles already in the system (#4493).
  • When only one MPI rank is used, the maximum cutoff of bonded interactions is ignored when initializing the cell properties, since the bond partners are always accessible on the same node, regardless of the cell size; if the system also doesn’t have short-range interactions, the short-range loop is skipped (#4452).
  • 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).
  • Reaction methods can delegate the particle neighbor search to the cell system when evaluating the exclusion range of inserted particles (#4401). This leads to better performance only on 2 or more MPI ranks.

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).
  • The OpenGL visualizer no longer raises an exception when activating the LB_draw_boundaries option without any other LB_draw_* option (#4479).
  • The OpenGL visualizer now correctly updates bond information when the collision detection and bond breakage features are used (#4502).
  • It is no longer possible to accidentally set a non-cubic NpT integrator with P3M (#4165).
  • The NpT integrator used to work with P3MGPU even though it didn’t implement long-range energy calculation and therefore couldn’t contribute to the virial; now the long-range energy is calculated and added to the virial (#4026, #4506).
  • Illegal LB node access is now properly caught by exceptions (#3978).
  • EK node access no longer accepts floating-point values for node indices (#4228), and always requires exactly three integers (#4482).
  • Accessing the flux property of EK species no longer throws an error (#4106).
  • Accessing the boundary field of LB nodes from a LBFluid actor when LB_BOUNDARIES is not compiled in now returns 0 instead of a random integer (#4479).
  • The LB grid in the GPU implementation is now automatically resized when the simulation box size changes (#4191).
  • The LB code now throws an error when adding a LB boundary to the LBFluid actor when LB_BOUNDARIES is not compiled in, or to the LBFluidGPU actor when LB_BOUNDARIES_GPU is not compiled in (#4472).
  • 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, #4492).
  • The system now throws an error when a non-bonded interaction cutoff is too large for the local box size in MPI-parallel simulations; in older releases the error was queued and deferred to the integration loop (#4479).
  • The system now throws an error when a virtual site tracks a real particle too far away for the local box size in MPI-parallel simulations; in older releases the error was queued and deferred to the integration loop (#4479).
  • It is no longer possible for a virtual site to track itself (#4479).
  • It is no longer possible for a particle to exclude itself (#4493).
  • It is no longer possible to accidentally add the same bond twice on the same particles (#4058).
  • Fatal errors triggered by stale references in virtual sites, invalid particle ids and null quaternions have become runtime exceptions (#4479).
  • Virtual sites now contribute to the rotational kinetic energy of the system (#4198).
  • Particle creation no longer raises numpy.VisibleDeprecationWarning (#4493).
  • The EK feature now generates VTK files that are compliant with the VTK 2.0 standard (#4106).
  • 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 now raises an exception when tuning fails instead of causing a fatal error (#4238).
  • The MMM1D actor now raises an exception for incorrect periodicity or cell system instead of causing a segfault (#4064).
  • The DipolarP3M checkpointing mechanism was fixed (#3879).
  • The DipolarP3M method now recalculates the energy correction when the box length changes (#4506).
  • 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).
  • 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).
  • Providing incorrect parameters to the ScaFaCoS actors no longer cause ESPResSo to crash (#4068).
  • FENE, harmonic and quartic bonds now throw an error when the bond length is zero and the equilibrium bond length is non-zero, since the direction of the force cannot be determined (#4471).
  • 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).
  • A bug in the collision detection feature that lead to a harmless warning being printed to the terminal upon collision was fixed (#4484).
  • Calling collision_detection.set_params() with invalid arguments no longer leaves the collision detection feature in an indeterminate state; the previous state is automatically rolled back (#4484).
  • Setting the collision detection mode glue_to_surface or bind_at_point_of_collision when feature VIRTUAL_SITES_RELATIVE is not compiled in now generates the correct error message (#4484).
  • 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 in 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/magnetostatic methods are no longer silently ignored at 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).
  • A bug that could potentially lead to stale references in the script interface was fixed (#4476).
  • TabulatedNonBonded.is_active() now returns False instead of None when the interaction is inactive (#3586).

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 CMakeLists.txt files are now formatted automatically with cmake-format (#3622).
  • The Python code and C++ code were checked with LGTM to detect and fix coding errors and anti-patterns (#3851, #3856, #4300).
  • Compiler warnings and diagnostics from GCC 11, 12, from Clang 10, 12, 13, 14 and from Intel 19.0.4 were addressed (#4084, #4426, #4510, #4526).
  • 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 into 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).
  • The LB coupling for the regular decomposition scheme was rewritten (#4470).
  • 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 custom MpiCallbacks framework has been simplified and the callbacks made more homogeneous (#4383).
  • The custom MpiCallbacks framework is being progressively replaced by boost::mpi communication (#4506, #4511).
  • 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), collision detection (#4484), reaction methods (#4451), MPI-IO (#4455), H5MD (#4480), cell system (#4511), actors, scafacos, electrostatics and magnetostatics (#4506). The corresponding Cython files were converted to Python files.
  • It is now possible to extend the list of available specifications in the H5MD feature at the C++ level (#4480).
  • 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.
  • Parameters can be passed to CTest at configuration time via the new CTEST_ARGS CMake option (#3862). This replaces the deprecated and non-portable ARGS Makefile variable expansion.
  • A superfluous and non-portable CMake target_compile_options() statement was removed (#3852).

Invitation to the ESPResSo Summer School 2021

Combining particle-based and continuum modelling in soft matter physics with ESPResSo, PyStencils, and LbmPy

Date:
Oct 11-15, 2021

Location:
online course (hybrid format)

Register:
https://www.cecam.org/workshop-details/1070

Schedule: PDF, iCalendar

Confirmed speakers

  • Friederike Schmid (University of Mainz)
  • Jens Harting (University of Erlangen–Nuremberg)
  • Markus Holzer (University of Erlangen–Nuremberg)
  • Marjolein Dijkstra (Utrecht University)
  • Ivan Cimrák (University of Žilina)
  • Peter Košovan (Charles University)

Notes from the Organizers

Due to restrictions related to the current Covid-19 situation, we have decided to offer the school mostly as an online event. If the Covid-rules applicable in autumn will permit, we might offer a small number of on-site places.

We will maintain the highly interactive format of the school. Lectures and talks will be streamed live on Zoom. Hands-on sessions will be tutored by experienced ESPResSo users and developers in small groups of participants, remotely via Zoom. There will be additional opportunities for scientific exchange during the user & developer meeting and the interactive talks.

The originally planned dates for the school are maintained. The coding sessions will take place in the afternoon, Central European Summer Time (UTC+02:00). Some tutoring groups could start later to accommodate for participants from different time zones, if there is sufficient interest.
 
Although this course is offered online, it is not designed as a MOOC: participation will be highly interactive, which limits the number of participants we can accept in the tutoring sessions. When registering for this course, please mention whether you are interested in taking part in the interactive tutorials, or if you are just interested in watching the lectures and talks.

Course description

In this school, participants learn to conduct simulations in the fields of statistical physics, soft matter and active matter using the software ESPResSo. It is an open-source particle-based simulation package with a focus on coarse-grained molecular dynamics models. In addition, it offers a wide range of schemes for solving electrostatics, magnetostatics, hydrodynamics and electrokinetics, as well as algorithms for active matter, rigid bodies, and chemical reactions[1].

ESPResSo consists of an MPI-parallelized simulation core written in C++ and a scripting interface in Python. This allows for good interoperability with other science and visualization tools for Python. ESPResSo can join forces with waLBerla, a high performance code for lattice-Boltzmann hydrodynamics and other lattice-based schemes for electrokinetics and related fields[2].

In this school, after an introduction to particle-based simulations and the simulation codes, we will focus on combining particle- and field-based approaches in simulations of soft matter. We will explore topics such as electrophoretic mobility of colloids, diffusion of polymers, and describing ions on the continuum level via electrokinetic equations.

We will provide an introduction to PyStencils[3] and LbmPy. These Python packages allow for the rapid prototyping of lattice-based algorithms, which can then be used together with waLBerla and ESPResSo. These packages are also used to generate the lattice-Boltzmann and electrokinetics kernels in ESPResSo.

Lectures will provide an introduction to the physics and simulation model building as well as an overview of the necessary simulation algorithms. During the afternoon, participants will practice running their own simulations in hands-on sessions. The teaching material will be provided electronically to the participants.

Many of the lectures and hands-on sessions will be taught by developers of the software. Hence, the school will also provide a platform for discussion between developers and users about the future of the software. Also, users can get advice on their specific simulation projects. The final day of the school will be dedicated to research talks on projects that have been conducted using ESPResSo and waLBerla.

Attendance to the summer school is free.

[1] F. Weik, R. Weeber, K. Szuttor, K. Breitsprecher, J. de Graaf, M. Kuron, J. Landsgesell, H. Menke, D. Sean, C. Holm, Eur. Phys. J. Spec. Top., 227, 1789-1816 (2019) DOI:10.1140/epjst/e2019-800186-9
[2] M. Bauer, S. Eibl, C. Godenschwager, N. Kohl, M. Kuron, C. Rettinger, F. Schornbaum, C. Schwarzmeier, D. Thönnes, H. Köstler, U. Rüde, Computers & Mathematics with Applications, 81, 478-501 (2021) DOI:10.1016/j.camwa.2020.01.007
[3] M. Bauer, J. Hötzer, D. Ernst, J. Hammer, M. Seiz, H. Hierl, J. Hönig, H. Köstler, G. Wellein, B. Nestler, U. Rüde, Code generation for massively parallel phase-field simulations. Published in: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (2019) DOI:10.1145/3295500.3356186

ESPResSo 4.1.4 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 4.1.3 and 4.1.4. 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

General corrections and improvements:

  • Fix a bug in the LB CPU implementation that lead to incorrect LB shear stress tensors in thermalized fluids since 4.1.0 (#3847)
  • Fix a bug in the LB CPU and GPU implementations that lead to gamma_bulk being used in place of gamma_shear in the second order term for forces in all previous ESPResSo versions (#3885)
  • Fix a bug that always set the epsilon value to zero in P3M and P3MGPU actors since 4.0.0 (#3869)
  • Fix an issue in the Python script interface that rejected integer epsilon values in the P3M and P3MGPU actors, and the 'metallic' epsilon value in the P3M actor (#3869)
  • Fix the exception mechanism in the P3M, P3MGPU and DipolarP3M code to forward errors to the Python interface instead of silencing them or running infinite loops (#3869)
  • Fix range checks in the OIF code that failed to raise TypeError exceptions (#3846)

Documentation and tutorials corrections and improvements:

  • Explain the discrepancy between the Gay-Berne formula from the user guide and from the original paper (#3839)
  • Add note explaining the P3M algorithm works with non-metallic epsilon values only when the box is cubic (#3869)

Build system and platform-related corrections and improvements:

  • Fix several CMake warnings raised by CMake 3.17 and above (#3830, #3859)

Improved testing:

  • Add a test to check the off-diagonal elements of the LB stress tensor in long simulations of thermalized fluids (#3847)

Under the hood changes:

  • Remove unnecessary memory allocation on GPU from MPI worker nodes (#3911)

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)

Under the hood changes:

  • Remove unused code (#3556, #3738)
  • Remove the unused FindPythonModule CMake module (#3736)
  • Update the espresso-ci bot scripts (#3613)

Invitation to the ESPResSo Summer School 2020

ESPResSo and Python: Versatile Tools for Soft Matter Research

Date:
Oct 5-9, 2020

Location:
online course

Register:
https://www.cecam.org/workshop-details/28

Schedule: PDF, iCalendar

Notes from the Organizers

Due to the uncertainty related to the current Covid-19 situation, we have decided to virtualize the school, although maintaining the highly interactive format. Hands-on sessions will be tutored by experienced ESPResSo users and developers in small groups of participants, remotely via videoconferencing. There will be additional opportunities for scientific exchange during the social event, the user & developer meeting and the interactive talks.

The originally planned dates for the school are maintained. The coding sessions will take place in the afternoon, Central European Summer Time (UTC+02:00). Some tutoring groups could start earlier or later to accommodate for participants from different time zones, if there is sufficient interest.

Although this course is offered online, it is not designed as a MOOC: participation will be highly interactive, which limits the number of participants we can accept in the tutoring sessions. When registering for this course, please mention whether you are interested in taking part in the tutoring, or if you’re just interested in watching the lectures and talks. The lectures and talks will be recorded and made available on our website after the event, accessible to everyone enrolled in this course.

Course description

In this school, participants learn to conduct simulations in the fields of statistical physics, soft matter and active matter using the software ESPResSo. It is an open-source particle-based simulation package with a focus on coarse-grained molecular dynamics models. In addition, it offers a wide range of schemes for solving electrostatics and magnetostatics, hydrodynamics, electrokinetics, as well as algorithms for active matter, rigid bodies, and chemical reactions. ESPResSo consists of an MPI-parallelized simulation core written in C++ and a scripting interface in Python. This allows for good interoperability with other science and visualization tools for Python.

After an introduction to particle-based simulations and the simulation software, a wide range of topics will be covered: colloids, gels, polymers, magnetic fluids, and active matter. Lectures will provide an introduction to the physics and simulation model building as well as an overview of the necessary simulation algorithms such as electrostatics and hydrodynamics solvers. During the afternoon, participants will practice running simulations in hands-on sessions with the help of developers of the software. Participants can also get advice on their specific simulation projects. The final day of the school will be dedicated to research talks on projects that have been conducted using ESPResSo.

Program:

  • Analysis and management of scientific data
  • Basic simulations in ESPResSo and Python
  • Understanding and quantifying simulation errors
  • Polymer melts
  • Polyelectrolyte electrophoresis
  • Colloids and gels
  • Long-range interactions, electrostatics, magnetostatics, P3M algorithm
  • Hydrodynamic interactions, lattice-Boltzmann method
  • Electrokinetics
  • Molecular dynamics
  • Rigid body mechanics, virtual sites
  • Magnetic fluids
  • Active matter
  • Monte Carlo

Attendance to the summer school is free.

ESPResSo 4.1.2 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 4.1.1 and 4.1.2. 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:

  • Remove correlation between the rotational noise and translational noise in the Langevin thermostat (#3355)
  • Fix a bug that may cause the wrong temperature to be set by the Langevin and DPD thermostats in the first time step after the system was altered from the Python level, e.g., by changing particles or interactions (#3341)
  • Fix a bug that caused the DPD thermostat to generate an incorrect velocity distribution when used together with the Langevin thermostat (#3352)
  • Fix a bug in MMM2D and ELC with potential boundary conditions, where one of the correction factors was over-counted resulting in wrong energies (#3310)
  • Fix a bug that caused the wrong bonds to be deleted when removing particles from the system (#3356)
  • Fix an ambiguity in ParticleSlice: the values in the square brackets refer to particle ids, not array indices (#3367). This means the ill-defined syntax system.part[0:-1] is no longer valid. See the User Guide section on Setting up particles for more information.
  • Remove the mass prefactor in the ComForce observable and use the correct Particle ids in the ParticleAngularVelocities and ParticleBodyVelocities observables (#3380)
  • Fix a rounding error that caused debug builds of ESPResSo running with multiple MPI threads to crash when a particle was placed exactly on the boundary between two cells (#3377)
  • Fix espressomd.has_features() for the corner case where the list of all compiled-in features is passed as argument, returning False instead of True (#3318)
  • Refactor the random number generator code (#3349)
  • Minor fixes (#3351, #3336)

Documentation and tutorials corrections and improvements:

  • Improve documentation of Monte Carlo methods (#3254, #3330)
  • Minor fixes (#3342, #3334)

Build system and platform-related corrections and improvements:

  • List all Python dependencies in requirements.txt with the supported version numbers (#3300). Please note that most of them are optional.
  • Add MPIEXEC_PREFLAGS and MPIEXEC_POSTFLAGS to the command lines of parallel tests (#3221)
  • Add the -oversubscribe flag to the command lines of parallel tests running with OpenMPI v2.X to avoid exiting early from a Python test configured without MAX_NUM_PROC on a machine with a hyperthreaded CPU where OpenMPI is configured such that the number of threads cannot exceed the number of cores (#3335)
  • Refactor the CI, maintainer, Doxygen and pypresso shell scripts to make them more portable and support filepaths containing whitespaces (#3326, #3373)
  • Fix a nvcc compiler warning on the empty config (#3329)

Improved testing:

  • Add a test for ELC and MMM2D using analytic expressions of the force and energy (#3331)
  • Sped-up seven Python tests (#3319)
  • Fix a test that broke on s390x architectures with Fedora 31 (#3312)
  • Fix tests that broke on i586 architectures with OpenSUSE Tumbleweed (#3327, #3358)

ESPResSo 4.1.1 released

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 released

This is a feature release, i.e., new functionality is added to Espresso. An additional focus of this release is quality assurance and modernization. The testing of Espresso’s functionality has been extended considerably. Also, sample and tutorial scripts are now automatically tested. Moreover, a large effort was put into modernizing the C++ simulation core. Work has been done, e.g., on particle sorting, the MPI communication infrastructure, and the lattice-Boltzmann implementations. Electrostatic and magnetostatic methods now have a clear and common interface. These changes will facilitate future extensions of Espresso and make the code more understandable to new developers.

We recommend that this release be used for all production simulations. No further bug fix releases will be provided for the 4.0 line, and not all fixes are present in Espresso 4.0.2.

Please carefully read the detailed list of changes below before using this release. The numbers in brackets refer to ticket numbers on https://github.com/espressomd/espresso.

Get it in the Download area

Changed requirements

  • Python 2 support has been dropped. Espresso now requires Python 3. For additional information, please see https://github.com/espressomd/espresso/wiki/python_2_3_transition.
  • Espresso now needs a C++14-capable compiler, such as GCC 4.9 and later or Clang 4 and later.
  • It is discouraged to use Espresso with Boost versions below 1.67.

Added functionality and documentation

  • The distance between a shape (such as sphere) and a position can now be queried via shape.calc_distance().
  • The lattice nodes of a lattice-Boltzmann fluid can now be iterated using LBFluid.nodes().
  • A tutorial on magnetic fluids has been added.
  • The stress created by the dissipative particle dynamics interaction (DPD) can now be obtained via the DPDStress observable.
  • The stress of a lattice-Boltzmann fluid can now be obtained via the LBFluidStress observable.
  • A torus shape has been added.
  • Two new accumulators for observables have been added: MeanVarianceCalculator and TimeSeries.
  • An ElectricPlaneWave constraint was added.
  • Experimental support for AMD GPUs via HIP. The future of this feature is unclear. Please do not base hardware buying decisions on its presence.
  • Visualization of slit pores in the OpenGL visualizer.
  • A Weeks-Chandler-Anderson short-range potential has been added (WCA).
  • The external force density applied to a lattice-Boltzmann fluid can now be changed during the simulation.
  • Sanity checks for Mach limits and unequal MD and lattice-Boltzmann time steps have been added.
  • The system.cell_system.tune_skin() method now has a keyword argument adjust_max_skin. If set to True, the maximum skin to be tested will be reduced such that it is compatible with the local box size.
  • For the CPU lattice-Boltzmann implementation, the limit on the Verlet list skin (<0.5 agrid) has been lifted.
  • A new observable CosPersistenceAngles has been added for the bond angles of a polymer (needed, e.g., for determining the persistence length).

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:
    • PARTIAL_PERIODIC
    • LB
    • LB_GPU (for builds with CUDA)
    • IMMERSED_BOUNDARY
    • BOND_ANGLE
  • For most compilers, it is checked that only known features are declared in myconfig.hpp.
  • The default feature configuration applied when no myconfig.hpp is present has been extended significantly. In particular, all tutorials can now be run with the default feature configuration. For production simulations, it is still recommended to use a custom myconfig.hpp containing only necessary features. This is true in particular, if particle rotation is not needed.
  • Features that do not have automated tests now require EXPERIMENTAL_FEATURES to be defined in myconfig.hpp.

Interface changes

Changed and removed functionality

  • The remove_total_momentum() method for lattice-Boltzmann fluids has been removed. The overall velocity of a fluid can be changed using the lb_fluid.nodes() iterator.
  • The CATALYTIC_REACTIONS feature has been removed.
  • The method for creating a polymer has been replaced. espressomd.polymer.positions() can now be used to obtain particle positions for one or more polymer chains.
  • Checkpointing has been added for the electrokinetics method.
  • The global random number seed has been partly replaced by method-specific ones. These are specified when activating the relevant feature such as the Langevin, DPD and lattice-Boltzmann thermostats via a seed keyword argument.
  • The random number generator has been switched to Philox for most algorithms requiring random numbers.
  • Limitations on the exclusion radius have been relaxed in the reaction ensemble method.
  • A new observable CosPersistenceAngles has been added for the bond angles of a polymer (needed, e.g., for determining the persistence length).
  • ELC has been disabled for non-neutral systems with constant potential.
  • The calculation of the linear particle momentum included the forces of the last time step. The function system.analysis.linear_momentum() now returns the sum of the product of mass and velocity of all particles, if no lattice-Boltzmann fluid is coupled.

Performance enhancements

  • Speedup in the short-range force calculation in situations where the short-range cutoff varies strongly for different pairs of particles, e.g., in a bidisperse fluid.
  • Speedup in particle resorting triggered when particles have moved by more than a skin.
  • Significantly faster back-transfer of particle forces from GPU-based methods such as the GPU implementations of lattice-Boltzmann and P3M.

Bug fixes

  • Lattice-Boltzmann boundaries, constraints and auto_update_accumulators are now included in checkpointing. (#2915)
  • Collision detection is now checkpointed. (#2342)
  • The rhomboid shape was fixed. (#2756)
  • Deadlocks on certain GPUs have been resolved for the dipolar Barnes-Hut method. (#2719)
  • The visualization of dihedrals has been fixed. (#2677)
  • The ENGINE implementation for CPU LB has been fixed. (#3025)
  • The external force density in lattice-Boltzmann fluids is no longer ignored in the first integration step after setting the force density. (#3144)
  • The positions of virtual sites and the charges of ICC particles are now updated before observable calculation. (#3128)
  • The forces and torques for the Gay-Berne potential have been corrected. (#3091)
  • Remove undocumented behaviour in the case of using a cylindrical sampling area in the reaction ensemble, constant pH ensemble, Wang-Landau ensemble, Widom-Insertion method. (#3174)
  • The ELC tuning error calculation has been rearranged to produce correct results for higher accuracies. (#3123)

New tutorials

  • Tutorials for simulating ferrofluids and for using the constant-pH method have been added.

Under the hood changes

  • Automated testing has been enhanced. It now also includes samples and tutorials. The overall test coverage for the simulation core has increased by ~12% since Espresso 4.0.2.
  • The CPU LB and LB-particle coupling have been refactored.
  • Particle resorting has been simplified and sped-up.
  • The MPI callback mechanism has been simplified. Furthermore, reduction operations such as summing values from all MPI ranks can now be performed.
  • Nearly all manual memory management and C-style arrays have been removed.
  • The rotation-related code has been simplified.
  • Long-range electrostatic and magnetostatic methods now have a common interface.
  • The kernels for short-range and bonded interactions have been simplified.
  • The CMake build system has been refactored and dependencies between different parts of the code have been made clear.
  • Python code formatting: the autopep8 version now matches the one in Ubuntu 18.04 (autopep8 v1.3.4 with pycodestyle v2.3.1).

ESPResSo 4.0.2 released


This release provides a number of corrections for the Espresso 4.0 line.
We recommend that this release be used for all production simulations.
Please note that a sign error in tabulated interactions was fixed.
Simulation scripts which worked around this problem might have to be changed.
Below, please find the list of changes. The numbers in brackets refer to
ticket numbers on http://github.com/espressomd/espresso. 

Get it in the Download area

Corrections for bugs that may harm simulation results:

  • A sign error in tabulated interactions was corrected such that
    the force equals the negative gradient of the potential (#2519,2520).
  • The flow field of the CPU lattice-Boltzmann implementation was deleted
    when aspects of the molecular dynamics cell grid were changed; E.g., when
    interactions, the skin or the parallelization setup were changed.
    ESPResSo now terminates with an error, when this happens.
    To avoid this, please setup the CPU lattice-Boltzmann after all
    other aspects of the system. The GPU LB is not affected in the 4.0
    release, but was affected in the current development branch (#2728, #2736).
  • Corrected the force acting on LB Boundaries for the case of
    agrid and density not equal to 1 (#2624).
  • Corrected the cutoff calculation for the soft sphere interaction. In the
    previous implementation, the offset parameter was ignored (#2505).
  • The “three point coupling” of particles to the lattice-Boltzmann method
    has been removed. While it works in most environments, for some compilers
    the calculation gives wrong values. This is likely caused by undefined
    behavior. A corrected implementation is available in
    ESPResSo’s development branch. It cannot be safely backported to 4.0.2,
    because the code has diverged too far (#2516, #2517).
    Users who did not explicitly activate this coupling via couple=”3pt” are
    not affected.
  • The velocity of existing particles was changed when setting or changing
    the simulation time step (#2480).

Further changes:

  • Fixed the electrokinetic Python interface (#2486)
  • Correction to the installation instructions for mac (#2510)
  • Corrected file permissions (#2470)
  • Minor corrections and extensions to the test suite (#2477, #2552)
  • Fixed a dead-lock in the dipolar Barnes Hutt method on the GPU for
    recent NVIDIA cards such as RTX 2080 (#2719).