Scientific Visualization

Scientific Visualization

The MPCDF provides a hardware and software infrastructure for remote visualization and supports Max Planck scientists in producing high quality scientific visualizations.

 

Services and Support

MPCDF operates a web-based remote visualization service (RVS) which enables users to access CPU and GPU resources and centrally managed visualization software (Paraview, VisIT, Blender, ...) for graphical analysis and of their data on HPC systems with their browser. Details can be found in the technical documentation on  Visualization

MPCDF supports Max Planck scientists in producing high quality scientific visualizations. For dedicated project support, please contact or 

Highlighted Visualization Projects

see also: complete list of  visualization projects

Encounters between rod-like phytoplankton cells in the ocean

Encounters between rod-like phytoplankton cells in the ocean

Physical scenario: Numerical modeling of encounters between rod-like phytoplankton cells in the ocean.
Simulations: J.-A. Arguedas-Leiva, C. C. Lalescu, M. Wilczek (MPI for Dynamics and Self-Organisation, MPCDF and University of Bayreuth)

Simulation code: TurTLE (Turbulence Tools: Lagrangian and Eulerian)

Visualisation approach (C. Lalescu, MPCDF, 2022):
  • main objective: visualisation of plankton dynamics in turbulence.
  • Intense vorticity structures are shown with a volume rendering - darker regions correspond to faster rotation of the fluid.
  • Cylinders represent individual rods (width increased tenfold for visibility).
  • tool: VTK (through Python wrapper)
  • animation (mp4, 58 MB)

References and further reading:
  • José-Agustín Arguedas-Leiva, Jonasz Słomka, Cristian C. Lalescu, Roman Stocker, and Michael Wilczek.Elongation enhances encounter rates between phytoplankton in  turbulence, PNAS 119 (32) e2203191119 (2022)
IAEA Crowdsourcing Challenge for Materials for Fusion Technology (Winning Team)

IAEA Crowdsourcing Challenge for Materials for Fusion Technology (Winning Team)

Physical scenario: Analysis of the wall material for the plasma vessel in a future fusion power plant simulating radiation damage in the crystalline structure of the material.
Simulations: U. von Toussaint, J. Dominguez   (Max-Planck-Institut für Plasmaphysik)

Main Codes:
  • Quippy (descriptor vectors) based on FORTRAN, Python, libAtoms and QUIP
  • Ovito (Interactive visualization of MD-data)
  • KDTREE2
  • voro++
Visualization approach (M. Rampp, M. Compostella - MPCDF, 2018):
  • main objectives: development of Python scripts for the visualization of defects in the lattice of the Tungsten and Steel crystals. Use of different RGB colour channels for the representation of different descriptors in the lattice. The final colour of each atom, given by the sum in the different channels, is shown together with cloud-like regions depicting voids in the damaged crystal.
  • tool: VisIt
References and further reading:
  • U. von Toussaint, F. J. Dominguez-Gutierrez, M. Compostella, M. Rampp. FaVAD: A software workflow for characterisation and visualizing of defects in crystalline structures  arXiv:2004.08184

Visualization of near-field effects in Quantum Nanoplasmonic Dimers

Visualization of near-field effects in Quantum Nanoplasmonic Dimers

Physical scenario: Dynamics of a dimer of Quantum Plasmonic Nanoparticles with 2x297 sodium atoms exposed to an external laser pulse.
Simulations: R. Jestädt, H. Appel (MPI for the Structure and Dynamics of Matter)
Simulation Code: OCTOPUS (Kohn–Sham density functional theory and time-dependent density functional theory calculations)
Visualization approach (M. Compostella, M. Rampp - MPCDF - & H. Appel - MPSD -, 2017):
  • main objectives: development of Python scripts for the visualization of real-time dynamics of complex systems exposed to external electromagnetic fields. Reconstruction of the laser pulse adopted in the OCTOPUS code. Possibility to compose several different views, static images and text labels into the same canvas. Automatic generation of frames for the entire time series running a single command line. Flexibility to produce an introductory movie that presents the physical context before showing the results of the time series.
  • tool: VisIt
References and further reading:
  • A. Varas, P. García-González, J. Feist, F.J. García-Vidal and A. Rubio, Quantum plasmonics: from jellium models to ab initio calculations, Nanophotonics, 5(3), pp. 409-426 (2017) (10.1515/nanoph-2015-0141)
  • A. Castro, H. Appel, Micael Oliveira, C.A. Rozzi, X. Andrade, F. Lorenzen, M.A.L. Marques, E.K.U. Gross, and A. Rubio, Octopus: a tool for the application of time-dependent density functional theory, Phys. Stat. Sol. B 243 2465-2488 (2006) (10.1002/pssb.200642067)
Reaction of CO2 molecule with CaO (001) surface

Reaction of CO2 molecule with CaO (001) surface

Physical scenario:
Adsorption of a CO2 molecule onto a CaO surface.
Simulations: A. Mazheika, S. V. Levchenko & M. Scheffler (Fritz-Haber-Institut)
Simulation Code: FHI-aims (Fritz Haber Institute ab initio molecular simulations)
Visualization approach (M. Compostella & M. Rampp, MPCDF, 2017):
  • main objectives: interactive data exploration, visualization of the modifications in the electron density during the interaction of a CO2 molecule with a CaO surface.
  • tools: VisIt, Blender
  • Download movie (1920x1080, 25 MB, MP4).
References and further reading:
Neutrino-driven core collapse supernova (Type-II) explosion in 3D

Neutrino-driven core collapse supernova (Type-II) explosion in 3D

Astrophysical scenario: Neutrino-driven explosion of a low-mass iron-core star
Simulation: T. Melson, A. Marek, F. Hanke & H.-Th. Janka (MPI for Astrophysics)
Simulation Code: VERTEX (3D Hydrodynamics & Boltzmann neutrino transport)
Visualization approach (E. Erastova & M. Rampp, RZG, 2014):
  • main objectives: interactive data exploration, visualization of the dynamics of large-scale hydrodynamical instabilities ("SASI")
  • tool: VisIt
References and further reading:

Talks and Training Material

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