• News

Published on July 7, 2022 by

A milestone in RheoCube’s evolution

RheoCube has grown as a solution and it's development has ramped up significantly in recent months. This major release comes with some fantastic improvements and new additions and it's with great excitement that we announce it today. While continuous improvement never stops, today marks a turning point in the evolution of this unique digital experimentation solution. Let’s take a look at what RheoCube version 1.0 has in store for you:

  • Redesign on RheoCube card homepage
  • Bulk export of ingredients
  • Improvements to RheoCube experiment workflow
  • Introduction of High Performance Computing
  • Model validation cases, and model improvements
  • Data Analysis and Visualization additions and improvements 

Redesign on RheoCube card homepage

We’ve implemented a new design to the project card view providing details on the most relevant information of the project.

Bulk export of ingredients

In addition to the single ingredient export functionality, you now also have the option to copy and transfer all ingredients from one project to another in one export. This also makes starting a new 1.0 project easier: you can copy all previously made ingredients into a new 1.0 project in one go.

This new feature translates into massive time savings across the product experimentation and development life cycle. 

All particles and/or fluids created can then be added to your project of choice. 

Improvements to RheoCube experiment workflow

We've introduced “enforced preprocessing for all cards” (which also allows for re-generating instances for that card). This is especially useful for the particle workflow. Preprocessing is now mandatory for all steps in the workflow. You’ll also see a new workflow that simplifies the input logic, in the following ways:

COMPOSITION

  • You’ll find a new Composition card view.
  • The “Molecular interaction theory” for meso scale simulations can now be chosen in Composition instead of Experiment. This is also the case with selecting the force-field version for molecular scale simulations.

FORMULATION

  • “Initial structure” is now available as an option to select from the top level drop-down menu in Formulation, resulting in all fields being directly relevant to the intended simulation setup. This selection is then also remembered as one moves through the workflow.
  • Molecular experiments (nanoscale molecular dynamics) can now also be selected from the same top level drop-down menu.
  • “Spatial resolution” (i.e. dx) is now located in Formulation, and will only show when setting up mesoscopic simulations.
  • When including particles in Formulation, we’ve included an additional option that allows for a specific number of particles to be added to the box as a numeric value (look for the option “Number” located under “Amount”). This option is automatically used for 1 and 2 particles as well as for droplet-particle structures. For experienced users: there is the option to specify the system size for molecular simulations. 

STATE

  • The input required in the State card has been reduced and improvements made to the workflow so that it's more intuitive . A few examples of these improvements are: 
    • When selecting "Initial structure" in Formulation, this selection can be further specified in State
    • The "volume fraction" from Formulation need no longer be re-entered in State
    • Molecular scale simulations no longer require input for State

EXPERIMENT

  • “Molecular interaction theory” has been removed as an option to select from Experiment, and instead now sits in Composition.
  • For experienced users: “Duration” and “Measurement” can now be specified for molecular simulations, as opposed to having to use the defaults.

Introduction of High Performance Computing

High Performance Computing (HPC) capabilities are now available on RheoCube. As the use of these instances in RheoCube are still being optimized, access will be granted on a case-by-case basis. 

Model validation cases

For RheoCube to have added value in research and development, the simulation results should be accurate, predictive and representative of what you will find should you do the same in the laboratory. Therefore, every simulation model used within RheoCube is put to the test by means of validation cases. This is done by choosing well established theories and/or well known experimental systems and making sure that the simulation models are able to capture the same behavior: 

  • At first qualitatively, in showing correct trends and dependencies; 
  • But ultimately quantitatively resulting in the same values for measurable properties.

The validation cases are chosen to represent well known behaviors in different types of complex fluids as well as in basic fluid systems. The results of these validation cases will now be included in the RheoCube manual. An overview of the current validation cases and their status can be found in the latest version of the manual, along with links to a description and proof of validation.

Molecular model improvements

New charged bead definitions have been added to the library of SDK beads (see the manual for a full list of available beads), meaning that the automatic coarse graining algorithm can now produce a limited number of ions and zwitterions for Coarse Grained Molecular Dynamics simulations that use the SDK force-field (SMILES input). 

The simulation protocols have also been adapted to handle the presence of charged beads (including Ewald summations for efficient calculations of the Coulomb interactions). Counter ions can be chosen (inorganic) or specified (organic) with the Add button below the SMILES input in the Fluid card. Ionics in molecular-scale simulations is now in RheoCube. The validation is qualitative and the full case description will be added at a later stage.

Data Analysis and Visualization

  • Molecule analysis widget

A widget for molecule analysis has been added. You can now plot molecule size and trajectory metrics, analyze the spatial distribution of molecules, and compute the diffusion constant of molecules.

Distribution plotting functions

The radial distribution function (RDF) computation has been significantly improved. Computing the RDF is now faster and the results correctly normalized. Instead of displaying the RDF as a histogram, it is now displayed as a line plot. The Pair Distribution Function has been renamed to the Pair Distribution (PD), but its functionality is unchanged.

  • Clustering widget split

The clustering widget is split into two widgets. One for clustering meso experiment results and one for clustering molecular experiment results.

  • Expanded parameter plotting

Many experiment constants previously inaccessible can now be plotted across experiments using the "Plot versus Parameter" functionality of the "Material Properties" widget. This includes ingredient properties, as long as the values are numerical and the ingredient is present in all of the experiments selected for comparison.

To be able to make full use of these new features, you will have to create a new 1.0 project in your environment. There will also be certain limitations around using version 0.5. 

We’re certainly over the moon with this 1.0 release achievement. It will see your R&D taken to a new dimension as RheoCube continues to bridge the gap between theoretical and physical science.

Let us know if you’re ready to upgrade your R&D environment.