Jean-Noël Grad

We are happy to announce the first release of pyMBE (doi:10.5281/zenodo.12102635), an open-source Python package designed to facilitate the design of custom coarse-grained models of polyelectrolytes, peptides and proteins in ESPResSo. pyMBE extends the ESPResSo API with methods to automate repetitive and error-prone tasks, such as setting up chemical bonds, non-bonded interactions and reaction methods.

pyMBE is maintained by an active community of soft matter researchers with a shared interest in the modeling of weak polyelectrolytes and biomacromolecules. We welcome new users and developers to join the project and contribute new features!

Learn more about pyMBE in our recent publication at The Journal of Chemical Physics (doi:10.1063/5.0216389), where we outline the main features of pyMBE and show how it can be leveraged in computational soft matter research.

This release provides a number of corrections for the ESPResSo 4.2 line. We recommend that this release be used for all production simulations. The interface has not been changed between ESPResSo 4.2.1 and 4.2.2. 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

Get the source code in the Download area.

Improved documentation

• Installation instructions now mention the FFTW3 MPI dependency of long-range solvers and provide recommended version numbers for Jupyter Notebook dependencies (#4790).
• Installation instructions now mention Python environments (#4922).
• Observables not properly document return values, array shapes, and use a more consistent mathematical notation (#4898).

Bug fixes

• Fatal runtime errors due to MPI global variables lifetime were addressed (#4858). Older ESPResSo releases built with Boost 1.84 or later might randomly crash when exiting the Python interpreter.
• Virtual sites no longer contribute to the kinetic energy of the system (#4839). The regression was introduced in April 2021 and affected the 4.2 branch of ESPResSo.
• Inertialess tracers are now integrated along the z-axis (#4714). The regression was introduced in February 2022 and affected the 4.2 branch of ESPResSo.
• Inertialess tracers now throw an exception when attempting to use LB GPU with 2 or more MPI ranks (#4714). Before, tracers on non-root MPI ranks would be silently ignored by the CUDA kernels, and would have a constant velocity, either 0 if the particle never visited the fluid domain on the root rank, or the last known velocity if the particle was once on the root rank. This bug affected all ESPResSo versions.
• Particles close to the faces of the simulation box are now properly coupled to the LB fluid (#4827). Due to numerical instability, it was previously possible for particles to be outside the box simulation by a tiny amount and skip LB particle coupling. The probability of this bug occurring was low, but could be enhanced in simulations that purposefully placed particle near the faces of the simulation box: polymers sheared by Lees-Edwards boundary conditions, raspberry particles (colloids, bacteria, etc.) when crossing a periodic boundary, or cell membranes placed close to a periodic boundary.
• Resizing the box now throws a runtime error if there are constraints present (#4778), since constraint preconditions might no longer be fulfilled. For example, a wall constraint might end up outside the box boundaries when the box shrinks.
• Resizing the box via system.box_l = new_box_l now throws a runtime error if there are particles present, because particle position folding cannot be guaranteed to be correct (#4901); use system.change_volume_and_rescale_particles() instead, which properly rescales particle positions.
• The velocity Verlet NpT propagator doesn’t apply friction and noise on angular velocities. ESPResSo now throws an error when NpT encounters a rotating particle (#4843). This bug affected all ESPResSo versions.
• The Brownian thermostat can no longer be configured with act_on_virtual=True due to an unresolved bug (#4295) that will be addressed in the next minor release.
• Restrictions on the number of MPI ranks have been lifted from the checkpointing mechanism (#4724). It is now possible to use checkpointing again in MPI-parallel simulations when the system contains LB boundaries or Union shape-based constraints. These restrictions had been introduced in 4.2.0 for technical reasons that have since been resolved.
• When passing an invalid value to a function that expects an input parameter of type list of size 3, an exception is now raised (#4911). Previously, some functions would print an error message and continue their execution with uninitialized data.
• The per-type and per-mol_id contributions from system.analysis.energy(), system.analysis.pressure() and system.analysis.pressure_tensor() now return the correct values (#4788). Older version of ESPResSo were confusing the particle mol_id with the particle type. The total pressure was unreliable when mol_id properties were set to non-zero values.
• The OpenGL visualizer now extracts the correct non-bonded potential parameter sigma when feature WCA is compiled in but LENNARD_JONES isn’t (#4720). The regression was introduced in 4.2.1.
• Method OifCell.elastic_forces() no longer throws a TypeError (#4813).
• Benchmark scripts were adjusted to support large particle numbers (#4753).

Under the hood changes

• Several Clang 16 and GCC 13 compiler diagnostics have been addressed (#4715).
• A non-critical GCC C++20 deprecation warning in Cython-generated code was disabled (#4725).
• Several deprecation warnings emitted by CMake 3.27 have been silenced (#4792).
• Add support for setuptools version 67.3.0 and above (#4709).
• Add support for Python 3.12 in testsuites run by CTest (#4852).
• Python requirements have been updated (#4924).
• CI pipeline URLs have been fixed (#4736).

Simulating soft matter across scales

Date:
October 7, 2024 – October 11, 2024

Location:
ICP, University of Stuttgart (Germany)

Register:
https://www.cecam.org/workshop-detail/1324

Schedule: PDF

Course description

Scientific content

This school will teach coarse-grained and lattice-based simulations methods suitable for modeling soft matter systems at mesoscopic length and time scales. We will explore topics such as simulating coarse-grained ionic liquids in electrolytic capacitors to measure differential capacitance, simulating coarse-grained liquids with machine-learned effective potentials to match the properties of models with atomistic resolution, polymer diffusion in an implicit solvent, particle coupling to continuum hydrodynamic fields, and diffusion-advection-reaction solvers for electrokinetics and catalysis.

Lectures will provide an introduction to the physics and model building of these systems as well as an overview of the necessary simulation algorithms. During the afternoon, participants will practice running their own simulations in tutored hands-on sessions using the software ESPResSo[1] and waLBerla[3]. 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 used in the hands-on sessions. Moreover, users can get advice on their specific simulation projects. Time will also be dedicated to research talks, which illustrate how the simulation models and software are applied, and which provide further background on soft matter at different length and time scales.

Poster session

As an on-site participant, you have the opportunity to bring a poster to introduce your work to your peers. We welcome abstract submissions on both planned and ongoing research projects, done with or without ESPResSo/waLBerla, as long as they fit to the general themes of this event. The abstract should contain at most 400 words without counting the bibliography, and not have been published elsewhere.

Everyone bringing a poster is invited to present it in a 1 minute lightning talk during the poster session. The poster boards will remain up for the entire duration of the school. Accepted contributions will be published in a book of abstracts under a permissive open-source license on Zenodo.

Invited speakers

• Timm Krüger, University of Edinburgh (United Kingdom)
• Tristan Bereau, University Heidelberg (Germany)
• Christine Peter, University of Konstanz (Germany)
• Frederik Hennig, University of Erlangen–Nuremberg (Germany)
• Matej Praprotnik, National Institute of Chemistry (Slovenia)
• Pablo M. Blanco, Norwegian University of Science and Technology (Norway)

Teaching material

Hands-on sessions

We use interactive Jupyter notebooks to teach concrete applications of the simulation methods introduced in the lectures. These notebooks outline physical systems relevant to soft matter physics and sketch simulation scripts written for the ESPResSo and waLBerla packages using the Python language. A few parts of these scripts are hidden and need to be completed by participants, with the help of the ESPResSo and waLBerla user guides and the tutors.

These exercises can also be carried out in self-study after the school via the online platforms Binder and Gitpod, and all exercises have hidden solutions that can be revealed at any time.

Software

In this school, participants learn to conduct coarse-grained and lattice-based simulations suitable for modeling soft matter systems using the software ESPResSo and waLBerla. ESPResSo 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[2]. These methods can be combined to simulate different scales and recover emergent material properties at macroscopic scales.

ESPResSo consists of an MPI-parallelized simulation core written in C++ and a scripting interface in Python which integrates well with scientific Python packages, such as numpy, pyMBE[5], pyOIF[6], ZnDraw[7] and SwarmRL[8]. ESPResSo relies on waLBerla, a high performance lattice-Boltzmann library, for hydrodynamics and other lattice-based schemes for electrokinetics and related fields[3]. Custom waLBerla kernels can be rapidly prototyped in symbolic form in Python and automatically converted to highly optimized, performance-portable code for CPUs and GPUs[4].

Event organization

This school is planned as an on-site event. We don’t charge a participation fee.

Hands-on sessions will be tutored by experienced ESPResSo/waLBerla users and developers. There will be additional opportunities for scientific exchange during the event: scientific speed dating and BBQ on Monday, poster session on Tuesday, city tour and conference dinner on Thursday.

A preliminary schedule is available as a PDF file in the Documents tab. A more detailed version will be made available in the summer, once all speakers have confirmed their time slots. The school starts on Monday at 9am and ends on Friday at 1pm.

References

[1] R. Weeber, J. Grad, D. Beyer, P. Blanco, P. Kreissl, A. Reinauer, I. Tischler, P. Košovan, C. Holm, ESPResSo, a Versatile Open-Source Software Package for Simulating Soft Matter Systems, 2023
[2] 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)
[3] 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)
[4] 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, 2019
[5] D. Beyer, P. B. Torres, S. P. Pineda, C. F. Narambuena, J.-N. Grad, P. Košovan and P. M. Blanco, 2024, arXiv:2401.14954 [cond-mat.soft]
[6] I. Jančigová, K. Kovalčíková, R. Weeber, I. Cimrák, PLoS. Comput. Biol., 16, e1008249 (2020)
[7] R. Elijošius, F. Zills, I. Batatia, S. W. Norwood, D. P. Kovács, C. Holm and G. Csányi, 2024, arXiv:2402.08708 [physics.chem-ph]
[8] S. Tovey, C. Lohrmann, T. Merkt, D. Zimmer, K. Nikolaou, S. Koppenhöfer, A. Bushmakina, J. Scheunemann, C. Holm, 2024, arXiv:2404.16388 [cs.RO]

Simulating energy materials with ESPResSo and waLBerla

Date:
October 9, 2023 – October 13, 2023

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/1229

Schedule: PDF, iCalendar

Course description

Scientific content

This school will teach the physics and simulation methods used to study energy materials. We will explore topics such as electrostatics in confinement, chemical reactions and catalysis, electrophoretic mobility, diffusion, and electrokinetics.

We will first introduce particle-based approaches and Monte Carlo schemes to model reactions in chemical systems. Then, 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 model building of these systems 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 physics of energy materials.

Poster session

As an on-site participant, you have the opportunity to bring a poster to introduce your work to your peers. We welcome submissions on both planned and ongoing research projects, done with or without ESPResSo, as long as they fit to the general themes of energy materials, fluid dynamics or soft matter physics.

Everyone bringing a poster is invited to present it in a 1 minute lightning talk during the poster session. The poster boards will remain up for the entire duration of the school.

Invited speakers

• Stephan Gekle (Universität Bayreuth, Germany)
• Timo Jacob (Ulm University, Germany)
• Laura Scalfi (Freie Universität Berlin, Germany)
• Peter Košovan (Charles University, Prague, Czech Republic)
• Céline Merlet (Toulouse III – Paul Sabatier University, France)
• Mathieu Salanne (Sorbonne University, Paris, France)
• Svyatoslav Kondrat (Institute of Physical Chemistry, Warsaw, Poland)

Teaching material

Hands-on sessions

We use interactive Jupyter notebooks to teach concrete applications of the simulation methods introduced in the lectures. These notebooks outline physical systems relevant to soft matter physics and sketch simulation scripts written for the ESPResSo package using the Python language. A few parts of these scripts are hidden and need to be completed by participants, with the help of the ESPResSo user guide and tutors.

We offer tutoring to all on-site participants and to a small number of online participants via Zoom. These exercises can also be carried out in self-study using the web browser via Binder or Gitpod, and all exercises have hidden solutions that can be revealed at any time.

Software

In this school, students learn to conduct coarse-grained and lattice-based simulations suitable for modeling energy materials, but which can easily be transferred to other fields of statistical physics and soft matter physics, using the software ESPResSo (espressomd.org) and waLBerla (walberla.net). ESPResSo 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].

Event organization

This school is primarily planned as an on-site event. Lectures and talks will be streamed live on Zoom for online participants. Hands-on sessions will be tutored by experienced ESPResSo users and developers. There will be additional opportunities for scientific exchange during the user & developer meeting, poster session, Q&A sessions and social events (scientific speed dating, BBQ, city tour, speakers’ dinner).

Attendance to the summer school is free.

References

[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

This release provides a number of corrections for the ESPResSo 4.2 line. We recommend that this release be used for all production simulations. The interface has not been changed between ESPResSo 4.2.0 and 4.2.1. However, some bugs were discovered which can affect simulation results.

We recommend that this release be used for all production simulations. No further bug fix releases will be provided for the 4.2 line.

Please find the list of changes below. The numbers in brackets refer to ticket numbers on https://github.com/espressomd/espresso

Get the source code in the Download area.

Added functionality

• P3M and DipolarP3M can now be used with the hybrid decomposition cell system with 1 MPI rank (#4678).
• Lattice-Boltzmann can now be used with the N-square and hybrid decomposition cell systems with 2 or more MPI ranks (#4676).

Changed requirements

• The nbconvert version requirement was bumped to 6.5.1 to patch an XSS vulnerability (#4658).

Improved documentation

• The user guide now documents how to improve the reproducibility of simulations that have checkpointing enabled (#4677).
• The user guide now reflects that the lattice-Boltzmann profile observables can be used in parallel (#4583).
• The active matter tutorial now uses an adequate engine dipole for the swimmer particle (#4585).
• The error analysis tutorials have been improved (#4597).
• The tutorials can now be used in VS Code Jupyter (both the desktop and web versions) and the mathematical formula are now correctly displayed (#4531).
• All ESPResSo-specific CMake options are now documented in the installation chapter of the user guide (#4608).
• Python package installation instructions no longer feature package version numbers; instead, requirements.txt is used as a constraint file (#4638).
• MMM1D algorithms now properly document their parameter names (#4677).
• Reaction methods now cite the relevant literature (#4681).
• Caveats for chain analysis methods are now documented (#4698).
• Minor formatting issues in Sphinx and typos in Python docstrings were addressed (#4608).

Interface changes

• A new boolean property System.virtual_sites.override_cutoff_check was introduced to allow disabling the cutoff range checks from virtual sites (#4623).

Removed functionality

• The unused and untested Analysis.v_kappa() method was removed (#4534).

Improved testing

• Improve unit testing of core functionality: P3M, MMM1D, OIF, virtual sites, script interface factory (#4631).

Bug fixes

• The checkpointing mechanism now properly restores the particle quaternion and all derived quantities (#4637). Release 4.2.0 introduced a regression that caused checkpoint files to overwrite the particle quaternion/director by a unit vector pointing along the z direction, when the DIPOLES feature was part of the myconfig file. This lead to incorrect trajectories when reloading a simulation from a checkpoint file, if the particle director played a role in the simulation (ex: relative virtual sites, Gay-Berne potential, anisotropic particles, active particles, etc.). In addition, the angular velocity in body frame was restored with the wrong orientation. Since the default myconfig file contains DIPOLES, most ESPResSo users were affected.
• The checkpointing mechanism now properly restores LB boundaries (#4649). Release 4.2.0 introduced a regression where reloading LB populations would accidentally reset LB boundary flags.
• The checkpointing mechanism now restores P3M and DipolarP3M solvers without triggering a re-tune (#4677). In previous releases, the checkpointing code would automatically re-tune these algorithms during a reload, causing tiny deviations in the forces that were problematic for trajectory reproducibility.
• Brownian dynamics now integrates the rotational dynamics of rotatable particles whose position is fixed in 3D space (#4548).
• Langevin dynamics now properly integrates particles with anisotropic friction (#4683, #4690).
• A regression that caused virtual sites to incorrectly count their image box when crossing a periodic boundary has been fixed (#4564, #4707).
• Particles can no longer be created or updated with a negative mass or a null mass (#4679).
• Particles created without a user-specified type can now participate in reactions (#4589).
• When a Monte Carlo displacement move is rejected, the original particle velocity is now restored (#4589).
• Reaction methods now raise an exception when accidentally calling method.reaction(steps=20) instead of method.reaction(reaction_steps=20) (#4666). Since 4.2.0 the steps argument was ignored, in which case the default value reaction_steps=1 would used by the core. Note that in the next minor release of ESPResSo, the reaction_steps argument will be renamed to steps.
• Reaction methods now rebuild the list of free particle ids every time WidomInsertion::calculate_particle_insertion_potential_energy() and ReactionAlgorithm::do_reaction() are called (#4609). This was needed to allow multiple concurrent reactions, as well as avoiding subtle bugs when both the user and a reaction method tried to create a new particle with an id that used to belong to a deleted particle.
• When all particles are cleared, the reaction methods type map is now also cleared (#4645). In the past, it was possible to attempt a reaction on particles that had just been cleared from the system, which would raise an exception. This bug affected all ESPResSo releases since 4.0.
• The System.part.pairs() method now returns the correct particle pairs when particle ids aren’t both contiguous and starting from 0 (#4628). The regression was introduced in release 4.2.0.
• The auto-exclusions feature no longer adds spurious exclusions to particle ids in the range 1, distance. This bug would potentially break the physics of the system and potentially raise an exception in a system with non-contiguous particle ids. This regression was introduced in release 2.2.0b.
• The structure factor analysis code no longer double-counts particles when the same particle type is provided twice (#4534).
• The minimal distance distribution analysis code no longer has an arbitrary cutoff distance when the simulation box is aperiodic (open boundaries); this would cause spurious artifacts to appear in the histogram at r = np.sum(system.box_l) when particles were further apart than this arbitrary distance (#4534).
• The cluster analysis functions are now disabled for systems with Lees-Edwards periodic boundaries, since the cluster analysis position wrapping code doesn’t properly handle the shear offset (#4698).
• The chain analysis methods now raise an error when the number of chains or beads per chain is invalid (#4708).
• The observable tests now longer rely on deprecated numpy options that were removed in numpy 1.24 (#4635).
• The visualizer *_arrows_type_materials options now have an effect on arrow materials (#4686).
• The visualizer exception handling mechanism has been made less brittle (#4686).
• The visualizer no longer raises exception when the optional dependency freeglut isn’t installed (#4691).
• The visualizer can randomly freeze when using collision detection or bond breakage; a temporary workaround has been introduced that fixes the issue for simulations that use only 1 MPI rank (#4686).
• The __dir__() method of script interface objects no longer raises an exception (#4674).
• Compilation and testsuite issues involving missing or incorrect feature guards were addressed (#4562, #4648).
• The build system no longer silently ignores invalid external feature definitions in myconfig.hpp and CMake files (#4608). This issue would only affect feature developers, as well as users of very old compilers, and would lead to ESPResSo builds missing features.

Under the hood changes

• The Clang 14 and AppleClang 14 compilers are now supported (#4601).
• Several Clang 14 compiler diagnostics have been addressed (#4606).
• Boost 1.81 and later versions are now supported (#4655).
• Compiler errors on non-x86 architectures were addressed (#4538).
• Test tolerances were adjusted for non-x86 architectures (#4708).
• The pypresso script now prints a warning when running with MCA binding policy “numa” on NUMA architectures that are not supported in singleton mode by Open MPI 4.x (#4607).
• The config file generator has been rewritten to properly handle external features and compiler errors (#4608).
• Security hardening for GitHub Workflows (#4577, #4638) and Codecov (#4600).
• Deployment of the user guide to GitHub Pages now relies on cloud providers to fetch JavaScript dependencies (#4656).

The Institute for Computational Physics at the University of Stuttgart is looking for a research software engineer to work on our open source simulation package ESPResSo.

Your tasks

• Coupling of particle-based algorithms like molecular dynamics to lattice-based ones such as lattice-Boltzmann
• Off-loading of parts of the computation to GPUs using CUDA
• Performance engineering, in particular with respect to parallelism and Monte Carlo methods
• Occasional contributions to other packages, e.g., the lattice-Boltzmann software Walberla/PyStencils/LbmPy used by ESPResSo for lattice-Boltzmann and diffusion-advection-reaction simulations
• Contributing to the maintenance of the molecular dynamics software ESPResSo, its documentation, and the continuous integration tooling

Your qualifications

• A strong interest in scientific software development and simulations
• An M.Sc. or Ph.D. in physics, computer science, simulation technology or a related discipline
• Proven experience in C++, experience in CUDA and Python are an asset
• Proven experience in numerical work such as simulations
• The willingness to engage with an interdisciplinary user and developer community
• The ability to pursue complex projects both, in teams and independently

What we offer

• A 12 to 18 months full time position (EG TV-L 13 with 39.5 hours/week)
• An exciting and friendly working environment
• Interesting and challenging development projects
• A well established CI/CD process including, e.g., automated testing and code review is in place
• Visibility of your work, as ESPResSo is an open-source project
• Frequent interactions with users of the software and the ability to foster your international network
• Ample opportunities for skill development, including e.g., training by the Stuttgart High Performance Computing Center (HLRS)
• Excellent compute resources

To apply

Please send your cover letter, CV and contacts for two references to application@icp.uni-stuttgart.de until May 15, 2023. If you have contributed to publicly hosted projects, please include links to your GitHub page or similar.

Diversity

At the University of Stuttgart, we actively promote diversity among our employees. We have set ourselves the goal of recruiting more female scientists and employing more people with an international background, as well as people with disabilities. We are therefore particularly pleased to receive applications from such people. Regardless, we welcome any good application.

Women who apply will be given preferential consideration in areas in which they are underrepresented, provided they have the same aptitude, qualifications and professional performance. Severely disabled applicants with equal qualifications will be given priority.

As a certified family-friendly university, we support the compatibility of work and family, and of professional and private life in general, through various flexible modules. We have an employee health management system that has won several awards and offer our employees a wide range of continuing education programs. We are consistently improving our accessibility. Our Welcome Center helps international scientists get started in Stuttgart. We support partners of new professors and managers with a dual-career program.

Information in accordance with Article 13 DS-GVO on the processing of applicant data can be found in German at https://careers.uni-stuttgart.de/content/Datenschutz/?locale=de_DE

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, iCal

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

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).

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

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)