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FIGURES from Visualization paper

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Fig. 1 - A collection of computational methods, and corresponding simulation tools, which are currently integrated to SimPhoNy, in addition to pre and post-processing as well as client-server solutions providing advanced control of intricate multiscale workflows.
Fig. 2 - Illustration of a possible data flow in an idealized multi-physics modelling case, where a fluid flow solver and a particle solver are coupled together using the SimPhoNy framework. Visualization of simulation data, with a chosen software tool, is possible either within the framework (using specific wrappers for the visualization tools) or externally after relying on integrated file-I/O tools for exporting the data to be visualized.
Fig. 3 - A schematic view of the various length (in meters) and time scales and some selected materials models that are typically used to describe phenomena at these length scales (in meters). The upper layer of images are l-r DFT at electronic scales (Quantum espresso/AViz see Figure 8, right), Atomic (Molecular Dynamics at atomic scale/AViz, see Figure 12), and Continuum (Kratos CFD, part of system, see Figure 23), Macroscopic scale, LB, entire system, see Figure 26). For visualization, scale is not the crucial part, rather it is the entity used in the model - electronic density, atomistic, mesoscopic or continuum.
Fig. 4 - View of AViz GUI: A diamond sample including the split interstial defect with bond thicknesses according to their length [8] and showing the AViz panels that were used to draw this sample.
Fig. 5 - Idealised flowchart of the NEMS project, covering simulations on electronic level to deduce the nanotube wall width, and on an atomistic level to obtain vibrational frequencies, for which the width estimate is needed [9].
Fig. 6 - These are two of many images from the scipy cookbook [23] in the Mayavi tips section, and shows a Mayavi interface in the upper frame with the color palette interface in the lower one. The image shows several ways to visualize the structure using both three dimensional and contour plots.
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Fig. 7 - View of nCAD GUI: assembly environment of nCAD, where several components are shown. The components have been slightly shifted along the Z axis for a better visualization. Bottom component shows a silicon with four holes where the nanocolumns of the next component fit. Different impurities have been used for each one. The elements here include cubic structured silcon, InAs, and graphite.
Fig. 8 - AViz visualization example of electronic density simulation data. The electronic density of wavefunction of a n=3, l=1, m=1 hydrogen atom state using binned color [12] (upper), and a stereo image of the electronic density of part of a nanotube [14] (lower).
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Fig. 9 - Mayavi visualization example. Electron localisation function of an H2O molecule. From Enthought Mayavi Documentation [21].
Fig. 10 - Two NCAD visualization examples of a subset of the Technion electronic density data, also shown in Figure 8. Upper: Gui with a quarter nanotube. Lower: enlarged planar view.
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Fig. 11 - AViz visualization example of atomistic simulation data. Upper: a spin visualization of a state in a 3D Heisenberg model data, color corresponding to z value, from [6]. Lower: A split interstitial defect in a diamond lattice [4], showing atoms colored according to their and their neigbours' coordination numbers and bonds colored according to the cooordination numbers of their neighbours.
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Fig. 12 - AViz visualization example of atomistic simulation data. An example of fovy (angle of viewing in the y direction) variation, with perspective above and a straight-on view at below, from [8]. The data is from a simulation of diamond (4-fold coordinated atoms in orange, with blue bonds) and 3-fold coordinated (graphitised) atoms in yellow.
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Fig. 13 - AViz visualization example of atomistic simulation data. Upper: An example of a nanotube in a red-cyan stereo view, from [10] Lower: An AViz vector field (magnetic field of a bar magnet) example from an undergraduate course project [11].
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Fig. 14 - AViz visualization example of liquid crystal simulation data. Upper: initial sample with crystals in random directions. Lower: sample after annealing into an ordered smectic state. Color corresponds to direction, from [16].
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Fig. 15 - Mayavi atomic visualization examples. Left: Hypothetical atomic structure to demonstrate Mayavi’s capability of visualising atoms and bonds. Colors depict a scalar data (e.g. mass) for each atom. From Enthought Mayavi Documentation [21].
Fig. 16 - Simple visualization examples with Paraview. Upper: particle example, where bonds are shown as white lines. Lower: mesh example, where colors show the temperature defined at each point.
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Fig. 17 - View of nCAD GUI showing the Atomic Editor where the user designs the atomic structure of individual components in an easy and guided workflow assisted by embedded visualization.
Fig. 18 - View of nCAD GUI (the Atomic Editor). Simultaneous visualization of four components formed by different allotrope forms of Carbon. Fullerene C60 (0D), double wall armchair carbon nanotube (1D), two layers of graphene (2D) and diamond structure (3D).
Fig. 19 - View of nCAD GUI (the atomic structure visualizers). Upper panel shows unit cell, material and component visualizers for silicon. Lower panel shows three different components with three visualizers for each one.
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Fig. 20 - View of nCAD GUI: atomic structure visualization in first person (gamer) mode, where the user can move across the structure.
Fig. 21 - nCAD GUI permits building different objects (angles, planes, distances, etc). Figure also shows the graphical gizmo for rotation and ruler that assists the movement.
Fig. 22 - Four examples of nCAD post-processing capabilities: a) Simultaneous representation of atoms and isosufaces; b) projection of different isosurfaces on spherical geometry; c) several colour maps; d) combined image using colour maps and projected isosufaces, exported in PNG format.
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Fig. 23 - Mayavi and Paraview visualization examples of continuum-model based simulation data. Upper: Visualization of a simulated pressured-driven flow in a tube (simulated with the Kratos CFD engine) using Mayavi; colors on the tube show the pressure values and vectors (and its color) show the velocity (and speed). Lower: Cubic lattice example visualised using Paraview.
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Fig. 24 - Simple visualization examples of structured data with Mayavi2: data is shown for a hexagonal lattice (left) and orthorhombic lattice (right). The orthorhombic lattice is represented using a simpler and more compact VTK dataset, made possible by the lattice’s high degree of symmetry.
Fig. 25 - Mayavi visualization example of continuum simulation data. Snapshots from the simulation of the water droplet (light blue isosurface) hitting the solid surface (grey isosurface) from time iterations a) 0, b) 100 , c) 200, d) 300, e) 400, and f) 500.
Fig. 26 - Paraview visualization example of continuum simulation data. Stream tracing (streamline) visualization of the water droplet which has hit the surface and is bouncing back. The red streamline color indicates the highest velocities which would be found nearest to the surface.
Fig. 27 - nFLUID geometry generation example: complex ad-hoc shape created with a set of positions.
Fig. 28 - View of nFluid GUI divided in four main windows: Channel Editor, List of Pieces, Channel Sketch, and advanced Visualizer.