=Paper=
{{Paper
|id=Vol-2023/244-251-paper-39
|storemode=property
|title= Activities related to scientific visualization at national research nuclear university "MEPHI", Moscow, Russia: research, education and publications
|pdfUrl=https://ceur-ws.org/Vol-2023/244-251-paper-39.pdf
|volume=Vol-2023
|authors=Victor Pilyugin,Evgeniya Malikova,Vladimir Adzhiev,Alexander Pasko,Galina Pasko,Igal Milman,Dmitry Popov
}}
== Activities related to scientific visualization at national research nuclear university "MEPHI", Moscow, Russia: research, education and publications==
https://ceur-ws.org/Vol-2023/244-251-paper-39.pdf
Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
ACTIVITIES RELATED TO SCIENTIFIC VISUALIZATION
AT NATIONAL RESEARCH NUCLEAR UNIVERSITY
"MEPHI", MOSCOW, RUSSIA: RESEARCH, EDUCATION
AND PUBLICATIONS
V.V. Pilyugin1, E.E. Malikova2, V.D. Adzhiev2, A.A. Pasko2,
G.I. Pasko3, I.E. Milman1, D.D. Popov1
1
National Research Nuclear University "MEPhI", 31, Kashirskoe shosse, Moscow, 115409, Russia
2
The National Centre for Computer Animation at Bournemouth University, Bournemouth University,
Talbot, Campus, Fern Barrow, Poole, Dorset, BH12 5BB, UK
3
Uformia AS, Industriveien 6, 9062 Furuflaten, Norway
E-mail: a VVPilyugin@mephi.ru
In this paper we present the results of scientific visualization research as a joint project of the NRNU
MEPhI (Moscow, Russia) and the National Centre for Computer Animation, Bournemouth
University (Bournemouth, United Kingdom). We consider scientific visualization as a modern
computer-based method of data analysis. The essence of this method is to establish the
correspondence between the analyzed initial data and their static or dynamic graphical interpretation
analyzed visually. The results of the analysis of graphical data are interpreted in terms of both the
initial data and the reality behind it. The method of scientific visualization as a method of scientific
data analysis is a method of spatial modeling of those data. It allows for utilizing enormous potential
abilities of a researcher and their spatial imaginary thinking in the process of data analysis. In the
general case, the process of data analysis using the method of scientific visualization can be quite
complex, iterative and interactive. This article is devoted to results of research and educational
projects. These projects are quite different and multidisciplinary. The goals of the data analysis can
be different as well. As a result, in most cases significantly different graphical representations can be
involved.
Keywords: scientific visualization, data analysis, multidimensional analysis, method of
scientific visualization, multisensory analysis, research and educational projects
© 2017 Victor V. Pilyugin, Evgeniya E. Malikova, Vladimir D. Adzhiev, Alexander A. Pasko,
Galina I. Pasko, Igal E. Milman, Dmitry D. Popov
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Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
1. Introduction
In this report, we would like to present the results of scientific visualization research as a
joint project of the NRNU MEPhI (Moscow, Russia) and the National Centre for Computer
Animation, Bournemouth University (Bournemouth, United Kingdom). We consider scientific
visualization as a modern computer-based method of data analysis [1]. The essence of this method is
to establish the correspondence between the analyzed initial data and their static or dynamic
graphical interpretation analyzed visually. The results of the analysis of graphical data are interpreted
in terms of both the initial data and the reality behind it (Fig. 1).
Figure 1. Scientific visualization method of data analysis
What does actually visual analysis of graphical data representation constitute? It is a matter
of principle to understand that qualitative visual analysis consists of the analysis of the spatial
interpretation correspond to the initial data. This means that the obtained graphical images serve just
as means for natural and convenient representation of the spatial interpretation to the researcher for
analysis. It is followed by the interpretation of the results in terms of the initial scientific data. Thus,
the method of scientific visualization as a method of scientific data analysis is a method of spatial
modeling of those data. It allows for utilizing enormous potential abilities of a researcher and their
spatial imaginary thinking in the process of data analysis. As the result of solving these problems,
some conclusions are made by the researcher regarding the spatial scene. As mentioned above, these
conclusions are then interpreted in terms of initial data. Thus conclusions are formed regarding the
object of study. In the general case, the process of data analysis using the method of scientific
visualization can be quite complex, iterative and interactive.
The works of mention above joint project in scientific visualization field are carried out in
three related directions:
Scientific Visualization of Physics Research,
Scientific Visualization in Physics Education,
“Scientific Visualization” Journal Publication.
We would like to underline that in all these directions we consider Scientific Visualization as
a method of data analysis.
2. Scientific Visualization in Physics Research
Nowadays mentioned above scientific visualization method is widely used by various
physics research groups at NRNU “MEPhI” [2]. The research is carried out by physics departments,
educational and scientific laboratory “Scientific Visualization” of NRNU MEPhI and NCCA of the
Bournemouth University.
A complex of software tools on base of different 3D modelling and visualization programs
(3DS Max[3], HyperFun[4], Jmol applet [5], VTK[6], Cortona3D[7]) was created as a result of this
collaboration. Interaction of different software components is shown in Fig. 2.
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Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
Figure 2. Interaction of the visualization software and the complex
a) A frame of animated visualization of the electron density field of nano-object N64
b) A frame of animated visualization of the dimer creation from 2 C20 fullerenes.
Figure 3. Examples of the nanostructure visualization
The main purpose of these programs is to provide researchers of joint university groups with
flexible research tools in their studies of such data as nanostructures and in multidimensional scalar
field visual analysis. As already noted, the research is closely connected to teaching. These tools
were designed to be used in research and education with development of appropriate e-leaning tools
including multimedia courses, virtual laboratory works and other materials. Some of these
educational projects will be described below.
Let’s consider some examples of the results obtained on base of the software complex.
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Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
2.1. 3D Studio Max
On Fig. 3 we presented an example visualization results of two application programs, written
on the basis of 3D Studio Max (3ds MAX). Noted that most of those programs were created as a
result of collaboration of the Scientific Visualization Laboratory with researchers from physics
departments of NRNU. The software is written in MaxScript and uses components of 3ds Max with
specially written plugins for scientific data visualization. The input data of the visualization software
were presented in specific data formats used by NRNU researchers Widely used nanostructure
descriptive formats XYZ, HIN, OUT, and MOL files. These files are output of some nanostructure
computer modelling software (HyperChem, Gamess [8, 9]) as well as applications written by
physicists of NRNU MEPhI [10].
2.2. Nanomodeller program
The “Nanomodeller” program was created as a result of collaboration of the Scientific
Visualization Laboratory with researchers from physics departments NRNU and researchers from
the Photochemistry Center of the Russian Academy of Sciences. It was developed and used by
researchers in their work on nanostructures modelling visualization and editing molecular structures
procedures [11]. An example of Nanomodeller functional procedure is presented on Fig.4.
Figure 4. Functional procedure in Nanomodeller – changing distance between two atoms
2.3. HyperFun+VTK project
HyperFun [4] and VTK [6] integration based project is a result of collaboration of the
Scientific Visualization Laboratory and NCCA of Bournemouth University. The results of this
collaboration are not only computer software program, but theoretical studies in modern scientific
visualization field trends as multidimensional and multisensory visualization [12, 18] and laboratory
works, that will be described in the next section.
Here, particular attention is paid to geometric model involved in scientific visualization to be
compact, precise and with unlimited complexity. The model is based on a constructive approach to
the creation of the function evaluation procedures of geometric shapes called the Function
Representation (FRep) [13]. Software program HyperFun is used to work with FRep modelling.
The software is mainly oriented to visualization of multidimensional scalar fields as results
of computer simulation. The studied scalar fields were given as functions of several variables defined
on domains represented as geometric objects that also could be defined by functions of several
variables. The visualization was made through the Visualization Toolkit (VTK) [6] based interface
for HyperFun [4]. Example of dynamic scalar field visualization is presented on Figs. 5.
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Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
Figure 5. Example of dynamic scalar field visualization. Visualization of dynamic electron
density field of С2H2 molecule
Examples of multisensory visualization of two scalar fields (electron density and electrostatic
potential fields of NCH molecule) are presented on Fig. 6: the collection of semi-transparent
isosurfaces, colored with values of second field and with several positions of the point sound source
(red sphere).
Figure 6. Screenshots of the interactive visual-auditory display of two scalar fields
The results of the visual and auditory rendering of the spatial scene are the following:
- a graphical image of projections of semi-transparent colored isosurfaces on a graphical
terminal;
- the point sound source represented by the red sphere with the sound source located in its
center. Its location is specified interactively by the user;
- sound wave generated by a sound terminal with the frequency corresponding to the value of
first field (electron density field) in point of location of the point sound source and perceived by the
user as a specific sound tone.
3. Scientific Visualization in Physics Education
Nowadays, it is especially important for students in physics to have skills in computer
modelling of physical objects and processes that can be very helpful in their research work. As
scientific visualization tools are widely used for analysis of computer modelling results, students in
physics are often taught to visualize results of computer modelling as well [15]. The described above
HyperFun+VTK software tool was used as a scientific visualization tool for analysis of various
physical objects and processes that are the results of computer modelling in educational and research
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Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
studies of students of physics departments at the NRNU "MEPhI". Laboratory practical materials
were created in support. Most often, the studied results of computer modelling are physical scalar
fields. Students are taught to consider different static and dynamic spatial images of computer
modeled scalar fields in the process of their analysis by means of scientific visualization. Some of the
results of scientific visualization problems solved by students as a part of their laboratory work are
presented on Fig.7.
Figure 7. Scientific visualization example of the order-parameter field for the second type
superconductor (Abrikosov vortices)
Different approaches to scalar field visualization:
a) isosurfaces;
b) volume visualization with the scalar field defined on a rectangular domain;
c) scalar field on a complex domain defined by one of the field's isosurfaces.
The field’s domain can be interactively cross-sectioned by the user with planes controlled by
white handles.
One more example is “The Scientific Visualization” course, which is taught to PhD students in
physics at the NRNU "MEPhI" [16, 17]. This course was developed by the Scientific Visualization
Laboratory with support of physics departments and the NCCA, Bournemouth University, UK. The
purpose of this course is studying theoretical principles of scientific visualization and acquisition of
practical skills in development of scientific visualization software. In general, the course aims to
develop the students’ spatial creative thinking while solving problems of scientific data analysis. So,
this course teaches students to consider and manipulate the corresponding spatial images, to make
their visual analysis and to interpret the analysis results in terms of the application area.
The course includes the following three sections: scientific visualization concepts and
capabilities, scientific visualization tools, and scientific visualization applications. All three sections
use the mentioned above software as an example. In the practical part of the course students write
software programs on the basis of the software complex mentioned in the Introduction.
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Proceedings of the XXVI International Symposium on Nuclear Electronics & Computing (NEC’2017)
Becici, Budva, Montenegro, September 25 - 29, 2017
4. “Scientific Visualization” Journal Publication
Figure 8. Main page of the “Scientific Visualization” Internet-journal
The NRNU “MEPhI” (Moscow, Russia) has been publishing the “Scientific Visualization”
Internet Journal (http://sv-journal.com) since 2009. Materials published in the Journal are devoted to
different aspects of computer scientific visualization development and application of its tools and
methods. Materials are published as papers and short communications. Authors may use English or
Russian as publication language. The title of an article, the list of authors and the abstract are
presented in both English and Russian languages. The primary aim of the Journal is to publish high
quality original works on computer scientific visualization. Previously published works are not
acceptable unless there is considerable update.
The editorial board consists of visualization specialists from Russia, USA, UK, Japan, France,
Singapore, Netherlands and Switzerland. The journal is indexed in Scopus, Compendex and Russian
Science Citation Index. We have to note that university researchers including PhD and master degree
students actively publish papers in the journal. Also, the journal is recommended as an educational
source for s PhD students of the mentioned “The Scientific Visualization” course.
5. Conclusion
As conclusion, we would like to say that scientific visualization attracts a lot of attention in the
NRNU "MEPhI", one of the leading Russian universities.
The works in this field are carried out in three related directions: Scientific Visualization in
Physics Research, Scientific Visualization in Physics Education and “Scientific Visualization”
Journal Publication.
These works are followed by research of theoretical aspects of modern Scientific Visualization
for scientific data analysis. All these activities are carried out in international collaboration with
involvement of leading Russian and foreign specialists.
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