Abstract
In this manuscript, we review the evolution of atomistic visualization over the last 12 years and put the development of the community in context with our own efforts within the DFG collaborative research center 716. The goal is to provide a comprehensive summary of all relevant work that has been conducted under the auspices of project D.3. In this project, we focused on the visualization and analysis of particle-based data sets, and on how to bring these visualizations onto the workstation of domain scientists without the need for a large rendering infrastructure. We discuss how our decisions and goals evolved over time and show the success stories and publications. Finally, we give an outlook on the challenges that still require additional research and to which extent the requirements and constraints of current research have changed the way visualization works after these 12 years.
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References
K. Engel, M. Kraus, T. Ertl, in Proceedings of Eurographics/SIGGRAPH Workshop on Graphics Hardware ’01(2001), pp. 9–16
J. Krueger, R. Westermann, in Proceedings of the 14th IEEE Visualization 2003 (VIS’03), VIS ’03 (2003), p.38
S. Stegmaier, M. Strengert, T. Klein, T. Ertl, in Fourth International Workshop on Volume Graphics, 2005 (2005), pp. 187–241
W. Qiao, D. Ebert, A. Entezari, M. Korkusinski, G. Klimeck, in VIS 05. IEEE Visualization, 2005(October 2005) , pp. 319–326
W. Qiao, M. McLennan, R. Kennell, D.S. Ebert, G. Klimeck, IEEE Trans. Visual. Comput. Graphics 12, 1061 (2006)
T. McLoughlin, R.S. Laramee, R. Peikert, F.H. Post, M. Chen, Comput. Graphics Forum 29, 1807 (2010)
W.T. Reeves, ACM SIGGRAPH Comput. Graphics 17, 359 (1983)
L. Westover, in Proceedings of the 1989 Chapel Hill workshop on Volume Visualization – VVS ’89 (1989), pp. 9–16
L. Westover, in ACM SIGGRAPH Computer Graphics, SIGGRAPH ’90 4 (1990), 24, pp. 367–376
R. Crawfis, N. Max, in Proceedings Visualization ’93(1993) , pp. 261–266
M. Gross, H. Pfister, editorsPoint-based graphics , in The Morgan Kaufmann series in computer graphics (Morgan Kaufmann, Amsterdam, Boston, 2007)
W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graphics 14, 33 (1996)
E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, T.E. Ferrin, J. Comput. Chem. 25, 1605 (2004)
W.L. Delano, CCP4 Newslett. Protein Crystallogr. 40, 82 (2002)
J. Ahrens, B. Geveci, C. Law, in Visualization handbook, edited by C. Johnson, C. Hansen (Elsevier, 2005), pp. 717–731
D. Stalling, M. Westerhoff, H.-C. Hege, in The visualization handbook , edited by C.D. Hansen, C.R. Johnson(Elsevier , 2005) , Chap. Amira: A H , 1, pp. 749–767
N. Max, J. Mol. Graphics Model. 23, 233 (2004)
C. Bajaj, P. Djeu, V. Siddavanahalli, A. Thane, in IEEE Visualization 2004 (2004) , pp. 243–250
J.A. Barker, D. Henderson, J. Chem. Phys. 47, 4714 (1967)
S. Gumhold, in Proceedings of Workshop on Vision, Modelling, and Visualization 2003 (November 2003) , pp. 245–252
T. Klein, T. Ertl, in Workshop on Vision, Modelling, and Visualization VMV ’04 (2004) , pp. 387–394
M. Horsch, J. Vrabec, M. Bernreuther, S. Grottel, G. Reina, A. Wix, K. Schaber, H. Hasse, J. Chem. Phys. 128, 164510 (2008)
G. Reina, T. Ertl, in Proceedings of Joint Eurographics – IEEE VGTC Symposium on Visualization 2005, K. Brodlie, D. Duke, K. Joy(2005) , pp. 177–182
K. Reda, A. Knoll, K.-I. Nomura, M.E. Papka, A.E. Johnson, J. Leigh, in ), 2013 IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) (2005) , pp. 59–65
R. Sicat, J. Krüger, T. Möller, M. Hadwiger, IEEE Trans. Visual. Comput. Graphics 20, 2417 (2014)
J. Amanatides, A. Woo, Eurographics 87, 3 (1987)
N. Lindow, D. Baum, H.-C. Hege, Comput. Graphics Forum 31, 1325 (2012)
M. Chen, Fourth International Workshop on Volume Graphics, 2005 (2005) , pp. 127–235
D. Chisnall, M. Chen, C. Hansen, Visual Comput. 23, 167 (2007)
M. Hopf, T. Ertl, in Proceedings of the 14th IEEE Visualization 2003 (2003) , pp. 433–440
R. Fraedrich, J. Schneider, R. Westermann, IEEE Trans. Visual. Comput. Graphics 15, 1251 (2009)
V. Springel, S.D. White, A. Jenkins, C.S. Frenk, N. Yoshida, L. Gao, J. Navarro, R. Thacker, D. Croton, J. Helly, J.A. Peacock, S. Cole, P. Thomas, H. Couchman, A. Evrard, J. Colberg, F. Pearce, Nature (2005) 435, 629
R. Fraedrich, S. Auer, R. Westermann, IEEE Trans. Visual. Comput. Graphics (2010) 16, 1533
H. Wang, L. Xiao, in Proceedings – 2016 International Conference on Virtual Reality and Visualization, ICVRV 2016 (September 2017) , pp. 197–203
K. Moreland, W. Kendall, T. Peterka, J. Huang, in Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis – SC ’11 (2011) , p. 10
S. Grottel, M. Krone, C. Müller, G. Reina, T. Ertl, IEEE Trans. Visual. Comput. Graphics 21, 201 (2015)
R. de Toledo, B. Levy, J.-C. Paul, Iterative methods for visualization of implicit surfaces on GPU, in Advances in Visual Computing. ISVC 2007, Lecture Notes in Computer Science (Springer, Berlin, Heidelberg, 2007) , pp.598_609
O. Fryazinov, A. Pasko, WSCG 2008, Communication Papers , 145 , 2008
A. Knoll, Y. Hijazi, A. Kensler, M. Schott, C. Hansen, H. Hagen, Comput. Graphics Forum 28, 26 (2009)
C.P. Gribble, T. Ize, A. Kensler, I. Wald, S.G. Parker, IEEE Trans. Visual. Comput. Graphics 13, 758 (2007)
A. Knoll, I. Wald, P.A. Navrátil, M.E. Papka, K.P. Gaither, in Proceedings of the 8th International Workshop on Ultrascale Visualization (ACM, 2013) (ACM, 2013) , p. 8
A. Knoll, I. Wald, P. Navratil, A. Bowen, K. Reda, M.E. Papka, K. Gaither, Comput. Graphics Forum 33, 71 (2014)
I. Wald, G. Johnson, J. Amstutz, C. Brownlee, A. Knoll, J. Jeffers, J. Gunther, P. Navratil, IEEE Trans. Visual. Comput. Graphics 23, 931 (2017)
I. Wald, A. Knoll, G.P. Johnson, W. Usher, V. Pascucci, M.E. Papka, in 2015 IEEE Scientific Visualization Conference (SciVis) (October 2015) , pp. 57–64
P. Navratil, J. Johnson, V. Bromm, IEEE Trans. Visual. Comput. Graphics 13, 1712 (2007)
S. Eichelbaum, G. Scheuermann, M. Hlawitschka, in EuroVis – Short Papers , edited by M. Hlawitschkaand T. Weinkauf(The Eurographics Association, 2013)
J. Staib, S. Grottel, S. Gumhold, Comput. Graphics Forum 34, 151 (2015)
W. Arndt, T.M. Asbury, W.J. Zheng, M. Mitman, J. Tang, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (2011) , pp. 936–938
M. Le Muzic, L. Autin, J. Parulek, I. Viola, in Eurographics Workshop on Visual Computing for Biomedicine , edited by K. Bühler, L. Linsen, N.W. John(The Eurographics Association, 2015), 2015, 61–70
J.E. Stone, K.L. Vandivort, K. Schulten, in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), LNCS, ISVC’11 PART 2 (Springer-Verlag, Berlin, Heidelberg, 2011) 6939, pp. 1–12
R. Fraedrich, R. Westermann, in Proceedings of IS & T/SPIE Electronic Imaging 2012, Conference on Visualization, Data Analysis, edited by P.C. Wong, D.L. Kao, M.C. Hao, C. Chen, R. Kosara, M.A. Livingston, J. Park, I. Roberts(January 2012), p. 82940Q
X. Tong, C. Li, H.-W. Shen, IEEE Trans. Visual. Comput. Graphics 23, 891 (2017)
A.C. Bauer, H. Abbasi, J. Ahrens, H. Childs, B. Geveci, S. Klasky, K. Moreland, P. O’Leary, V. Vishwanath, B. Whitlock, E.W. Bethel, Comput. Graphics Forum 35, 577 (2016)
H. Yu, C. Wang, R.W. Grout, J.H. Chen, K.-L. Ma, IEEE Comput. Graphics App. 30, 45 (2010)
J. Wei, H. Yu, R.W. Grout, J.H. Chen, K.-L. Ma, IEEE Comput. Graphics App. 32, 22 (2012)
J. Woodring, J. Ahrens, J. Figg, J. Wendelberger, S. Habib, K. Heitmann, Comput. Graphics Forum EuroVis 30, 1151 (2011)
S. Rizzi, M. Hereld, J. Insley, M.E. Papka, T. Uram, V. Vishwanath, in International Conference for High Performance Computing, Networking, Storage and Analysis, PGV ’15 (2014) , pp. 8–9
W. Usher, I. Wald, A. Knoll, M. Papka, V. Pascucci, Supercomput. Front. Innovations 3, 4 (2016)
S. Grottel, G. Reina, in 2009 IEEE Pacific Visualization Symposium (April 2009) , pp. 65–72
M. Falk, S. Grottel, M. Krone, G. Reina, Synth. Lectures Visual. 4, 1 (2016)
S. Grottel, G. Reina, C. Dachsbacher, T. Ertl, Comput. Graphics Forum 29, 953 (2010)
P. Boudier, G. Sellers, ARB_conservative_depth(2011)
S.W. Skillman, M.S. Warren, M.J. Turk, R.H. Wechsler, D.E. Holz, P.M. Sutter arXiv:1407.2600 (2014)
K. Schatz, C. Muller, M. Krone, J. Schneider, G. Reina, T. Ertl, in IEEE Symposium on Large Data Analysis and Visualization 2016, LDAV 2016 – Proceedings (October 2017) , pp. 56–64
A. Panagiotidis, G. Reina, M. Burch, T. Pfannkuch, T. Ertl, in Proceedings of the 8th International Symposium on Visual Information Communication and Interaction – VINCI ’15 (2015) , pp. 35–41
S. Frey, G. Reina, T. Ertl, in Proceedings – 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing, PDP 2012(February 2012) , Biomedicine Workshop , pp. 399–406
P. Gralka, S. Grottel, G. Reina, T. Ertl, in IEEE Symposium on Large Data Analysis and Visualization 2013, LDAV 2013 – Proceedings (October 2013 , pp. 85–93
T. Rau, M. Krone, G. Reina, T. Ertl, in SIBGRAPI, 30th Conference on Graphics, Patterns and Images (2017)
P. Gralka, C. Schulz, G. Reina, D. Weiskopf, T. Ertl, in Proceedings – 2017 IEEE Working Conference on Software Visualization, VISSOFT 2017 (September 2017 , pp.54–63
D. Bruening, Efficient, Transparent, and Comprehensive Runtime Code Manipulation (Massachusetts Institute of Technology, Cambridge, MA, USA, 2004)
C. Müller, S. Grottel, T. Ertl, Image-space GPU metaballs for time-dependent particle data sets, in In Vision, Modelling and Visualization (VMV ‘07) (2007)2007 , pp. 31–40
M. Falk, S. Grottel, T. Ertl, in Proceedings of SIGRAD 2010: Content Aggregation and Visualization (2010) , pp. 35–43
S. Grottel, M. Krone, K. Scharnowski, T. Ertl, in IEEE Pacific Visualization Symposium 2012, PacificVis 2012 – Proceedings 2012 , pp. 209–216
M. Krone, G. Reina, S. Zahn, T. Tremel, C. Bahnmuller, T. Ertl, in IEEE Pacific Visualization Symposium (April 2017) , pp. 275–279
S. Grottel, G. Reina, T. Zauner, R. Hilfer, T. Ertl, in Proceedings of the Annual SIGRAD Conference (2010) 45–51
D. Kauker, M. Krone, A. Panagiotidis, G. Reina, T. Ertl, Comput. Visual. Sci. 15, 111 (2012)
D. Kauker, M. Krone, A. Panagiotidis, G. Reina, T. Ertl, in Proceedings of the 13th Eurographics Symposium on Parallel Graphics and Visualization (2013) , pp. 33–40
D. Kauker, M. Falk, G. Reina, A. Ynnerman, T. Ertl, Comput. Visual Media 2, 45 (2016)
M. Ibrahim, P. Wickenhauser, P. Rautek, G. Reina, M. Hadwiger, IEEE Trans. Visual. Comput. Graphics 24, 944 (2018)
L.-Q. Yan, M. Hašan, W. Jakob, J. Lawrence, S. Marschner, R. Ramamoorthi, ACM Transactions on Graphics 33, 1 (2014)
P.J. Basser, C. Pierpaoli, J. Magn. Reson. B 111, 209 (1996)
S. Grottel, P. Beck, C. Muller, G. Reina, J. Roth, H.R. Trebin, T. Ertl, IEEE Trans. Visual. Comput. Graphics 18, 2061 (2012)
S. Grottel, G. Reina, J. Vrabec, T. Ertl, IEEE Trans. Visual. Comput. Graphics 13, 1624 (2007)
K. Bidmon, S. Grottel, F. Bös, J. Pleiss, T. Ertl, Comput. Graphics Forum 27, 935 (2008)
S. Frey, T. Schlömer, S. Grottel, C. Dachsbacher, O. Deussen, T. Ertl, in IEEE Pacific Visualization Symposium 2011, Pacific Vis 2011 – Proceedings (March 2011 , pp. 51–58
M. Balzer, T. Schlömer, O. Deussen, ACM Trans. Graphics (Proceedings of SIGGRAPH 2009) 28, 86 (2009)
B. Thomaß, J. Walter, M. Krone, H. Hasse, T. Ertl, in International Workshop on Vision, Modeling and Visualization (2011) , 16 , pp. 301–308
C. Müller, M. Krone, K. Scharnowski, G. Reina, T. Ertl, in Proceedings of the 8th International Symposium on Visual Information Communication and Interaction – VINCI ’15 (2015) , pp. 131–136
P. Gralka, S. Grottel, J. Staib, K. Schatz, G. Karch, M. Hirschler, M. Krone, G. Reina, S. Gumhold, T. Ertl, IEEE Comput. Graphics App. 38, 106 (2018)
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Reina, G., Gralka, P. & Ertl, T. A decade of particle-based scientific visualization. Eur. Phys. J. Spec. Top. 227, 1705–1723 (2019). https://doi.org/10.1140/epjst/e2019-800172-4
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DOI: https://doi.org/10.1140/epjst/e2019-800172-4