Proceedings 2022 ESPResSo meetings

Proceedings of the 2022 ESPResSo meetings

2022-05-24

Planned features for the 4.3.0 release

• reaction methods
  • more efficient MD/MC coupling is needed
  • checkpointing (roadmap in #4154)
  • converting Gibbs ensemble to C++ probably not necessary, unless it can benefit from parallelization
• packaging for pip: the Boost MPI and CUDA dependencies may be an issue
• auto-update accumulators with error analysis
  • the Boost Statistical Accumulators Library currently only supports uncorrelated samples
  • statistical tools for correlated time series (binning analysis, jackknife, etc.) require visual inspection
  • it is safer to write the observable as a time series to disk and do the error analysis separately
• modular FFT implementation
  • allows using high-performance FFT libraries that support OpenMP
• particle storage rewrite
  • separate forces/torques from the particle struct for more efficient integration loop
• system propagation rewrite
  • propagation scheme stored on the particle (#4259)
  • offers more flexibility for rigid bodies, virtual sites and particles coupled to a lattice-Boltzmann fluid
• multi-system simulations
  • almost all global variables have been removed in 4.2.0 (#2628)
  • currently remaining globals: box geometry, cell structure, thermostats, Verlet skin, time step, simulation time, CUDA device memory pointers, etc.

Program of the 2023 summer school

• main topic: energy materials
• topics for lectures: electrokinetics, catalysis, electrostatics in slab geometries, grand canonical ensemble with potential
• topics for tutorials: 2D electrostatics (ELCIC), fluctuating electrokinetics
• proposal submission deadline: 17 July 2022

2022-05-03

Refactoring of electrostatics/magnetostatics methods

• replace Cython interface by a Python interface with C++ script interface
• P3M on GPU now implements energies by re-using the CPU kernel
• P3M on GPU is now compatible with ELC
• CPU methods no longer rely on global variables
• issues with ELC energies in Grand canonical ensemble w/ contrasts

Future of the mayavi visualizer

• not actively maintained, is missing several components (e.g. shaped-based constraints)
• installation: dependency tree is broken on ICP workstations
• no known users at the ICP

Program of the 2022 summer school

• CECAM page: Simulating the dynamics of soft matter with ESPResSo, PyStencils and LbmPy, October 10, 2022 - October 14, 2022
• planned content, pending approval from speakers:
  • external lectures: lbmpy/pystencils (Markus Holzer), lattice-Boltzmann (Timm Krüger), Lees-Edwards (Sebastian Bindgen), charged polymers (Peter Košovan)
  • internal lectures: active matter (Christoph Lohrmann), charged systems (Alex Schlaich), polymer electrophoresis or translocation in nanopores (Christian Holm), basic error estimation in observables and time series (Jean-Noël Grad), data management intro lecture + exercise with e.g. pandas (Rudolf Weeber)
  • scientific talks: Ulf Schiller, Andreas Hartel, Sabine Klapp

2022-04-12

ESPResSo 4.2.0 release

• all features need to be checked after the feature freeze
  • port 4.1 scripts to 4.2 to check for regressions
  • send feedback to the core team
• assignments
  • Christoph: GPU LB and swimmers
  • Patrick: magnetization curves
  • Alex: electrostatics
  • Ingo: EK, collision detection
  • Mariano: cluster analysis (script from Sebastian)
  • David: reaction methods
  • Julian: OpenGL

Lees-Edwards

• particle LEbc in 4.2.0
• fluid LEbc in 4.3.0
• shear profile needs to be checked against analytical solutions for special cases (e.g. polymers)

Program of the 2022 summer school

• new lecture: Lees-Edwards
• hybrid event with 1 online tutorial group in the morning

Program of the 2023 summer school

• energy materials, multiscale simulations

Tag der Wissenschaft

• polymer with MIDI board
• billiards game
• chamber game (entropy)
• PyStar for the GUI

2022-02-08

Refactoring actors as ScriptInterface classes

• required to remove global variables in the core
• required to replace Cython files by Python files
• progress:
  • reaction ensemble: 90% completed (Pablo, JN)
  • magnetostatics: 80% completed (JN)
  • electrostatics: just started (JN)
  • lattice-Boltzmann: 100% complete in the walberla branch (Rudolf, JN)
  • electrokinetics: python interface in progress (Alex)

Coding day progress report

• DomainDecomposition renamed to RegularDecomposition
• Particle property getters implementation (ready for review)
  • pre-requisite for octree decomposition (MD load balancing)
• walberla progress
  • GPU kernels implemented, macroscopic value accessors still missing
  • Lees-Edwards prototype mostly complete in the walberla bridge, next steps:
    • merge the MD part of Lees-Edwards into the python branch
    • then merge LB part of Lees-Edwards in the walberla branch
  • electrokinetics: reaction kernels to be implemented

2022-01-18

Format of the 2022 school

• current plan is to hold the event onsite
  • postpone decision on alternative formats (online or hybrid)
• if onsite: allow for small? online group for participants from further away (6-7 persons per tutor)
  • maybe make one "beginners"-group
  • maybe two different groups with different levels
    • formulation on what we expect from the "expert" level

Coding day

• Friday, February 4th

Re-organization of the particle storage

• rework particle storage such that "hot" properties are stored in a cache line
• Rudolf worked on a prototype with different particle types:
  1. current Particle struct from ESPResSo 4.2-dev (poor performance)
  2. flat particle struct with reordered properties to optimize padding (better performance)
  3. particle-pool where the particle only has an index to a struct-of-arrays (SoA) structure (best performance)
• next step: start with abstracting particle-property access (should be done anyhow)
• Rudolf will continue to tinker -> Cell-system resorts need to be reflected in the SoA

Lees-Edwards

• now correctly implemented in waLBerla
• next step is to integrate it in the ESPResSo waLBerla bridge