- Atomistic Vizualization
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- Atomistic Vizualization AViz, [1.2] is a C++ and OpenGL/mesa based public domain package designed to visualize large numbers of atoms, vector spins, quadrupoles and other solid objects. Its application in dot mode to the visualization of electronic density is described in a companion poster, here we concentrate on visualization of three dimensional systems of solid objects, whose locations and (where applicable) directions or polymer connections are calculated in advance or in parallel with a wide range of simulation or enumeration tools. AViz differs from many other excellent existing visualization tools in that it was created by physicists interested in the study of defects, amorphous systems and sample melting with the philosophy that no predefined bond lengths, connections or angles exist. Bonds are actually concentrations of high electronic density, but the basic information concerns object locations (and directions if the object is a spin or a quadrupole). Cylindrical bonds can and are constructed as a guide to the eye for depth comprehension, or drawn to aid recognition of localpe. atomic coordination, but are only one of many tools for helping to understand sample structures. Nathan Franklin and Adham Hashibon, Fraunhofer IWM, Freiburg, Germany Jeremy Rutman, Amihai Silverman and Joan Adler -Technion, Haifa, Israel, [1] https://github.com/simphony/AViz [2] http://phony1.technion.ac.il/~aviz [3] J. Adler, Y. Koenka and A. Silverman, Physics Procedia, 2011, 15, 7; data from P. Pine, Y. Yaish and J. Adler, PRB (2011) 83, 155410. [4] P. Bavli, E. Polturak and J. Adler, PRB (2011), 84, 235442. [5] D. Saada, J. Adler and R. Kalish, InT. J. Mod. Phys, C, (1998) 9, 61. [6] A. Silverman, J. Adler, and R. Kalish, PRB (2011), 83, 224206. [7] R. Hihinashvilli, J. Adler, S.H. Tsai and D.P. Landau, in``Recent Developments in Computer Simulation Studies in CMP, XVII'', (2004) 169. [8] J. Adler, H. Glanz, and N. Izrael, Physics Procedia, (2014), 57c, 2. [9] http://phelafel.technion.ac.il/~shyuv/, data from S. Srebnik. ACKNOWLEDGEMENTS: The latest version of AViz is part of the EU-SimPhoNy project. The research leading to these results has received funding from the European Union's Seventh Framework Programme under grant agreement no [604005]. Nano-related examples are shown above, where the use of slice-indicate-only (upper left) and of drawing only bonds of specific sizes [3] (upper right) are invoked to illustrate nanotube bending. Two applications of color variation are presented to illustrate layer mixing in melting magnesium [4] before and after heating (at left) and in the image below left we show color selection of differently coordinated atoms and bond lengths to show defect formation [5]. Further examples of color variation for different carbon hybridizations are given below. The latest version of AViz can be found on the SimPhoNy github pages [1] and a new website [2] (above) contains examples and tutorials. Within the framework of SimPhoNy effort has already gone into streamlining the source compilation process, and in material to support installers who may not be systems experts. We may wish to alter the perspective (fovy, 2 views at right) [6] or in order to show lattice structure, we may wish to only draw lattice bonds (upper right), and sometimes a simulation model has non- atomic alternative objects such as spins [7] or liquid crystal [8]. We might want to retain the connectivity of a polymer (wrapped around a nanotube in this case [9]), lower left. In both the spin (center below) and liquid crystal case (lower right) color is used to indicate direction through an AViz panel, whereas in the other images color is preselected and introduced via the elements panel.
Transcript of - Atomistic Vizualization
- Atomistic Vizualization
AViz, [1.2] is a C++ and OpenGL/mesa based publicdomain package designed to visualize large numbers ofatoms, vector spins, quadrupoles and other solid objects. Itsapplication in dot mode to the visualization of electronicdensity is described in a companion poster, here weconcentrate on visualization of three dimensional systemsof solid objects, whose locations and (where applicable)directions or polymer connections are calculated in advanceor in parallel with a wide range of simulation orenumeration tools.
AViz differs from many other excellent existing visualizationtools in that it was created by physicists interested in thestudy of defects, amorphous systems and sample meltingwith the philosophy that no predefined bond lengths,connections or angles exist. Bonds are actuallyconcentrations of high electronic density, but the basicinformation concerns object locations (and directions if theobject is a spin or a quadrupole). Cylindrical bonds canand are constructed as a guide to the eye for depthcomprehension, or drawn to aid recognition of localpe.atomic coordination, but are only one of many tools forhelping to understand sample structures.
Nathan Franklin and Adham Hashibon, Fraunhofer IWM, Freiburg, Germany
Jeremy Rutman, Amihai Silverman and Joan Adler -Technion, Haifa, Israel,
[1] https://github.com/simphony/AViz[2] http://phony1.technion.ac.il/~aviz[3] J. Adler, Y. Koenka and A. Silverman,Physics Procedia, 2011, 15, 7; data from P. Pine, Y. Yaish and J. Adler,PRB (2011) 83, 155410.[4] P. Bavli, E. Polturak and J. Adler, PRB (2011), 84, 235442.[5] D. Saada, J. Adler and R. Kalish, InT. J. Mod. Phys, C, (1998) 9, 61.[6] A. Silverman, J. Adler, and R. Kalish, PRB (2011), 83, 224206.[7] R. Hihinashvilli, J. Adler, S.H. Tsai and D.P. Landau, in``Recent Developmentsin Computer Simulation Studies in CMP, XVII'', (2004) 169.[8] J. Adler, H. Glanz, and N. Izrael, Physics Procedia, (2014), 57c, 2.[9] http://phelafel.technion.ac.il/~shyuv/,data from S. Srebnik.
ACKNOWLEDGEMENTS: The latest versionof AViz is part of the EU-SimPhoNy project.The research leading to these results hasreceived funding from the European Union'sSeventh Framework Programme under grantagreement no [604005].
Nano-related examples are shown above, where the useof slice-indicate-only (upper left) and of drawing onlybonds of specific sizes [3] (upper right) are invoked toillustrate nanotube bending. Two applications of colorvariation are presented to illustrate layer mixing in meltingmagnesium [4] before and after heating (at left) and inthe image below left we show color selection of differentlycoordinated atoms and bond lengths to show defectformation [5]. Further examples of color variation fordifferent carbon hybridizations are given below.
The latest version of AViz can be found on the SimPhoNygithub pages [1] and a new website [2] (above) containsexamples and tutorials. Within the framework of SimPhoNyeffort has already gone into streamlining the sourcecompilation process, and in material to support installerswho may not be systems experts.
We may wish to alter the perspective (fovy, 2 viewsat right) [6] or in order to show lattice structure,we may wish to only draw lattice bonds (upperright), and sometimes a simulation model has non-atomic alternative objects such as spins [7] orliquid crystal [8]. We might want to retain theconnectivity of a polymer (wrapped around ananotube in this case [9]), lower left. In both thespin (center below) and liquid crystal case (lowerright) color is used to indicate direction through anAViz panel, whereas in the other images color ispreselected and introduced via the elements panel.
