Using multiple softwares for performing a simulation

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annier
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Re: Using multiple softwares for performing a simulation

Post by annier »

Installation of Texlive in Ubuntu 14.04
http://tex.stackexchange.com/questions/ ... re-missing
http://tex.stackexchange.com/questions/ ... -or-ubuntu
http://tex.stackexchange.com/questions/ ... -file?rq=1
http://tex.stackexchange.com/questions/ ... tu-12?rq=1

1. Things to go for if one does a lot of hit-and-trials to fix "dot_sty file missing" and the original configuration of texlive is messed up

In summary, if one gets messed up with the configuration of texlive in Ubuntu and faces situations with "dot_sty files missing", then the previous installation can be cleaned up according to:
Removing things related to texlive for fresh installation in Ubuntu
and a fresh installation can be done in accordance to:
1.

Code: Select all

$ sudo apt-get install texlive-full
With this the texlive-full 2013.20140215-1 is installed (till this date)

or,

2. https://www.tug.org/texlive/quickinstall.html

2.Solution for "ccmap.sty not found " in Ubuntu 14.04 provided that texlive is installed from Ubuntu software package (step 1 as above)
a. Download ccmap.sty file from http://lsec.cc.ac.cn/cgi-bin/viewcvs.cg ... /ccmap.sty and keep the file within any directory ABCD.
b. Make a directory with the name ccmap in /usr/share/texmf/tex/latex/ directory.

Code: Select all

$ sudo mkdir /usr/share/texmf/tex/latex/ccmap
c. Jump into the directory ABCD and copy the ccmap.sty file from the directory ABCD to the newly made ccmap directory.

Code: Select all

$ sudo cp ccmap.sty /usr/share/texmf/tex/latex/ccmap
d. Update the Latex Package cache.

Code: Select all

$ sudo texhash
Reference:
http://makandracards.com/makandra/29089 ... untu-14-04
https://help.ubuntu.com/community/LaTeX
http://askubuntu.com/questions/632246/x ... pst-3dplot
https://www.tug.org/xetex/
http://tex.stackexchange.com/questions/ ... untu-12-04
http://tex.stackexchange.com/questions/ ... o-function


Yours Sincerely
Anil Kunwar
Last edited by annier on 23 Jan 2016, 17:35, edited 5 times in total.
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
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Re: Using multiple softwares for performing a simulation

Post by annier »

Last edited by annier on 20 Feb 2016, 15:53, edited 21 times in total.
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
mzenker
Posts: 1999
Joined: 07 Dec 2009, 11:49
Location: Germany

Re: Using multiple softwares for performing a simulation

Post by mzenker »

Hi,

there is a very comfortable LaTeX frontend (in fact it is a document processor based on LaTeX) called LyX: http://www.lyx.org. I have used it for my thesis back in 2000/2001 and I liked it very much. It is still actively developed and has certainly evolved since that time. Unfortunately I cannot use it any more since my company insists that we use M$ products... :(
But for people using LaTeX anyway it is worth a try!

Matthias
annier
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Joined: 27 Aug 2013, 13:51
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Re: Using multiple softwares for performing a simulation

Post by annier »

Hi Matthias,
Lyx is a very nice platform for editing latex files and compiling them. Thank you for sharing your experiences.

Yours Sincerely
Anil Kunwar
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

Updating Texlive in Ubuntu 14.04
1. Initialize Texlive Package Manager (tlmgr) using the following command:

Code: Select all

$ tlmgr init-usertree
Reference:
http://tex.stackexchange.com/questions/ ... etup-tlpdb

2. Install package decompressor "xzdec" using Ubuntu software center.

3. Update the Texlive including the tlmgr itself using the command:

Code: Select all

$ tlmgr update --self --all
References
http://www.tug.org/texlive/doc/tlmgr.html#EXAMPLES
http://www.tug.org/texlive/tlmgr.html
http://tex.stackexchange.com/questions/ ... -in-ubuntu
http://tex.stackexchange.com/questions/ ... stribution

4. Install perl module providing the Tk graphics "perl-tk" library using Ubuntu software center. (useful for running

Code: Select all

$ tlmgr --gui
)


Upgrading Texlive from 2013 to 2014 in Ubuntu 14.04

Installing Vanilla texlive in Ubuntu
This is a very robust installation step or procedure in Ubuntu.

Debian packages of texlive
https://packages.debian.org/search?keywords=texlive

Ubuntu packages of texlive
http://packages.ubuntu.com/wily/all/texlive/download

http://askubuntu.com/questions/568230/a ... l-it-every

XeLatex and Fontspec Related Things
fontspec how to handle it in ctex
xetex fontspec not found
fontspec information with xelatex
textsuperscript and hash symbol
lualetex query with fontspec
[xelatex] fontspec error: "font-not-found" ! in arch-linux forum
xelatex and lualatex about fontspec topic
using the texlive fonts in xelatex
laursen's thesis template in xetex
kerkis font working together with xelatex manual installation
fontspec features for xelatex and lualatex
ligature_tex syntax in xetex
latex plus new fonts is equal to xelatex

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I was fascinated when I saw that xelatex can use all the new fonts like Asana Math, Cambria (for text and math), Calibri etc, and I need not learn anything new apart from my existing latex understanding. This blog is the summary of my efforts in installing xelatex and the new fonts and making them work on my Ubuntu 10.04 machine!

First of all, for xelatex and the new fonts to work, one should have the latest tex distribution. Unfortunately Ubuntu 10.04 still have only texlive 2009. So the first step would be to acquire texlive 2010 and install it. Once it is done, the rest is trivial. Again installing texlive 2010 is also very easy – straightforward for at least Ubuntu.

1 (a). Installing TeXLive 2010 from a CD
One can get an iso image of TeXLive 2010 from the TeXLive Site. Once the iso image is burned into a DVD, you can do the following for installation.
You may need the perl-tk package before you start. You can install this on ubuntu by the command sudo aptitude install perl-tk . I got this information from the blog How to install TeXLive 2010 on Ubuntu 10.10
Once  you have installed perl-tk, and the DVD ready, you can follow the detailed instructions on the blog How to install Vanilla TexLive 2010 on Ubuntu 10.04.
Make sure to rename your local texmf tree if you have one. I forgot to do this and it created lot of difficulties for me.
1(b) Installing TeXLive 2010 from Internet
Go to this site.

2. Updating TeXLive 2010
First you have change the repository from which tlmgr would do the updates. It is done by the command,
tlmgr option repository http://mirror.ctan.org/systems/texlive/tlnet

Now you have to update tlmgr itself, if needed. Run the command tlmgr update --self to update the tlmgr itself.
Once tlmgr is updated, you can run tlmgr update -all to install all updates. Beware, it will take some time, even to start dumping messages on the screen.
3. Where to put microsoft/other fonts in texlive?
If your platform is windows, you can skip this step and go to section 4. If you are on a Ubuntu machine, you will not have access to the Microsoft fonts in the machine. You need to have the ttf files of the microsoft windows if you want to use them with latex.  Once  you get the font files, this is how you would install them. Getting the font files is described in the next section.

TeXlive will have a texmf-local folder inside your texlive installation. Inside that a fonts directory is present. Whatever ttf files you get hold of, you can create a directory inside the texmf-local/fonts/ and store the ttf files. For example I have the following directories there: texlive/texmf-local/fonts/vista, texlive/texmf-local/fonts/comic, texlive/texmf-local/fonts/Bergamo, texlive/texmf-local/fonts/sorts-mill-goudy, texlive/texmf-local/fonts/sorts-mill-goudy, texlive/texmf-local/fonts/STIXv1.0.0 etc.
After installing new fonts, you have to run the command fc-cache -fv from your home directory.
4. How to get the microsoft fonts for use in Ubuntu/LaTeX?
You may use any of the method described below:

Using your flash drive, copy the font files from windows and follow the steps in section 3.
Read Install Free Office 2007 Fonts for Linux and XP.
5. You are done! Ready to test the comic font now
\documentclass[12pt]{article}
\usepackage{fontspec}
\usepackage{amsmath}
\usepackage{unicode-math}
\usepackage{lipsum}
\setromanfont{Comic Sans MS}
\setmathfont{XITS}
\begin{document}
\begin{equation}
x = \frac{-b \pm \sqrt{b^2 – 4ac}}{2a}
\end{equation}
\lipsum[1]
\end{document}

You can copy the above code from here

+ expand source
This is the output on my machine!
6. How to compile the above code?
Save the above file as test.tex
xelatex test.tex
View the pdf file in your favourite pdf viewer!
7. Some Explanations for the LaTeX code
\usepackage{fontspec}: Allows  you to put arbitrary fonts using the command \setromanfont{font family name} . For example \setromanfont{Comic Sans MS}
\usepackage{unicode-math}: Allows you to put arbitrary math font using the command, for example,\setmathfont{XITS}
8. How to find the Font Family name?
In windows, this is easy, but in Ubuntu, you can use the command otfinfo. For example, otfinfo --family STIXVarBol.otf gave me the family name as STIXVariants which I can use in the setromanfont or setmathfont commands.

9. Acknowledgement
When I got stuck, many in the comp.text.tex and xetex mailing list helped me. I want to particularly thank, Will Robertson, who is the author of the fontspec and unicode-math packages.
figuring out xetex fonts under debian
notes on latex xelatex by alex krispin
chinese fonts in xelatex in ubuntu 14_04

Code: Select all

LaTeX中文的另一個方式 – XeLaTeX for Chinese (Windows & Ubuntu 10.04 – 14.04)
posted in Word Processor	by Wan-rong Jih
English

使用XeTeX撰寫中文的LaTeX文件

以前在LaTeX中,若要使用中文,是使用Big5碼的方式,第一次需要先安裝中文字型,中文文件要先以CJKconv轉換,再以bg5LaTex處理(詳見此文)。這幾年開始使用XeLaTeX,只需要有xeCJK package不論是Windows MikTeX或者是Ubuntu的TeXLive都可以使用,而且在不同的作業系統也能使用同樣的中文字型,讓LaTeX的中文文件可以在Windows及Ubuntu都可以直接使用不需做調整,真的方便很多。

以下是一個很簡單的中文sample.tex檔案,在完成XeLaTeX的設置後,可做為測試之用。

\documentclass{article}
\usepackage{fontspec} 
\usepackage{xeCJK} 
\XeTeXlinebreaklocale "zh" 
\XeTeXlinebreakskip = 0pt plus 1pt 
%Select fonts
\setmainfont[Mapping=tex-text]{Times New Roman} % rm
\setsansfont[Mapping=tex-text]{Arial}           % sf
\setmonofont{Courier New}                       % tt
\setCJKmainfont{DFKai-SB} %xelatex 標楷體
\setCJKmonofont{MingLiU}  %xelatex 細明體
%...
\begin{document}
中文字的測試
\end{document}
Windows MikTeX:

在Windows要在LaTeX裏使用中文,只要安裝MikTeX就可以了。不論是MikTeX 2.8或是2.9均能使用 xelatex sample.tex 來產生包含中文的PDF檔案。

Ubuntu TexLive:

因為我的LaTeX範例是使用Windows的中文字型,所以需要另外安裝字型。我並沒有特別使用任何指令執行安裝字型,而是直接把Windows的字型複製到Ubuntu的字型資料匣中。Windows 7到8.1的字型資料都是在C:\Windows\Fonts下。我在Ubuntu時,先將Windows硬碟mount上來,再將所有的Windows字型均複製至Ubuntu的系統字型資料匣/usr/local/share/fonts中。複製完資料後,只要再確認一下資料的存取權限是否與Ubuntu原有字型的存取權限相同就一切OK了。剛安裝字型時,若XeTeX仍找不到字型,可以使用sudo fc-cache -f -v更新字型,或者試試重新開機。

此外,因為Ubuntu的系統字型目錄需要管理者權限才能執行,所以,若無管理者權限,也可以把Windows的字型複製到個人的~/.fonts資料匣下。

關於安裝TexLive的部份,我是以Synaptic勾選texlive、texlive-latex-base、texlive-latex-extra及texlive-latex-recommended。當然,也可以直接安裝texlive-full。

texlive和字型都安裝完成後,只要執行指令 xelatex sample.tex 便能產生有中文字的PDF檔案了。

Update 2015-09-04:  原本文章中沒有中文的說明,最近安裝Windows 8.1及Ubuntu 14.04後,重新測試並補上中文說明。

REFERENCE

中研院數學所TeX Tools網站。
Chinese

Type Chinese in LaTeX – XeLaTeX and the xeCJK Package

Compare with CJK in LaTeX, the xeCJK package of XeLaTeX is much easy to use for  Chinese characters.  Most of LaTeX distributions support  XeLaTeX, such as the MikTex in Windows, the TeXLive in Ubuntu.

A sample file sample.tex contains Chinese characters:

\documentclass{article}
\usepackage{fontspec} 
\usepackage{xeCJK} 
\XeTeXlinebreaklocale "zh" 
\XeTeXlinebreakskip = 0pt plus 1pt 
%Select fonts
\setmainfont[Mapping=tex-text]{Times New Roman} % rm
\setsansfont[Mapping=tex-text]{Arial}           % sf
\setmonofont{Courier New}                       % tt
\setCJKmainfont{DFKai-SB} %xelatex 標楷體
\setCJKmonofont{MingLiU}  %xelatex 細明體
%...
\begin{document}
中文字的測試
\end{document}
Windows MikTeX:

Simply use the command xelatex sample.tex can create a PDF file.

Ubuntu TexLive:

The LaTeX command \setCJKmainfont in sample.tex, the DFKai-SB and MingLiU are True Type fonts (TTF) fonts from Microsoft Windows.  Ubuntu users can download these .ttf files from any free download site, e.g. DFKai-SB from FontZone and MingLiU from fontpalace.  Copy these two .ttf files to the  directory /usr/local/share/fonts/  (default font directory for all users, require admin authorization) or ~/.fonts/ (for yourself use only), to make the XeLaTeX can find the suitable fonts.

After get the Chinese fonts, you can use the command xelatex sample.tex to create your PDF files in Chinese.

Update 2015-09-04: This still works for Ubuntu 14.04. You can mount the Windows partition, and copy all files from the Windows font folder (…/Windows/Fonts) to the Ubuntu new fonts folder (/usr/local/share/fonts) (or your local fonts folder (~/.fonts)). In addition, please remember to check the permissions of files. If you cannot make things work, you may need to execute the command sudo fc-cache -f -v to refresh the font cache, or you can simply reboot the computer.
installing cjk fonts in ubuntu
Illustration for mentioning cjk fonts in xelatex in ubuntu
tex from an academician from Wuhan University
http://mvcdecoder.googlecode.com/svn/tr ... ct/thesis/

Thesis Templates for Some Universities
1. BUAA
2. scut or SCUT and code google
3. DLUT
4. FDUThesis
Last edited by annier on 20 Feb 2016, 17:02, edited 19 times in total.
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

Hi All,
Desktop recorder in ubuntu software center
http://www.researchgate.net/post/Does_a ... te_physics

solving the /var/lib/dpkg/lock in ubuntu
1. http://sourcedigit.com/15249-how-to-fix ... k-problem/
2. http://askubuntu.com/questions/423143/s ... you-root-e
3. https://bugs.launchpad.net/ubuntu/+sour ... bug/349469
4. https://wiki.edubuntu.org/DebuggingInstallationIssues

subprocess usr_bin_dpkg how to handle it
1. http://www.linuxquestions.org/questions ... -a-171107/

Adding microsoft core fonts in ubuntu
1.in howtogeek
2. in techtalkz
3. in pcworld with graphical illustration
4. in ubuntuforums
5. in superuser
6. microsoft fonts in embraceubuntu
7. vista fonts in embraceubuntu
8. install windows vista fonts in the linux system
9. libreoffice and some fonts

fonts in ubuntu repository
1. https://help.ubuntu.com/community/Fonts
2. http://chinese.stackexchange.com/questi ... -for-comme
3. http://wenq.org/wqy2/index.cgi?action=b ... me&lang=en
4. http://bbs.ctex.org/forum.php?mod=viewthread&tid=57755
5. http://ubuntuforums.org/showthread.php?t=900810
6. http://tex.stackexchange.com/questions/ ... e-in-latex
7. http://www.ece.uci.edu/~chou/unicode-tex.html

launchpad repository in ubuntu
1. https://www.wikihow.com/Install-Tor-on-Linux
2. https://www.linuxquestions.org/question ... 175572171/
3. https://askubuntu.com/questions/6522/how-to-install-tor
4. https://www.torproject.org/download/dow ... l.en#linux
5. https://askubuntu.com/questions/514853/ ... -04/515148
6. https://askubuntu.com/questions/382394/ ... -in-ubuntu
7. https://www.linuxhelp.com/how-to-instal ... in-ubuntu/
8. http://www.webupd8.org/2013/12/tor-brow ... m=referral
9. https://www.tuicool.com/articles/AJZnMnY
10. https://www.linuxhint.com/install-tor-b ... nt-ubuntu/
11. http://www.lupaworld.com/thread-977042-1-1.html
12. https://github.com/TheTorProject/gettor ... tag/v7.0.6
13. https://www.ctolib.com/TheTorProject-gettorbrowser.html
14. https://torrentproject.se/17c8fb69ab4b1 ... rrent.html



Yours Sincerely
Anil Kunwar
Last edited by annier on 20 Oct 2017, 19:25, edited 14 times in total.
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

Hi,
Effects of diffusion and length in passive advection
Oxygen transport description by advection diffusion equation
https://www.comsol.com/multiphysics/what-is-convection
https://www.comsol.com/multiphysics/con ... n-equation
https://ceprofs.civil.tamu.edu/ssocolof ... ok/Ch2.pdf
http://www.erc.uct.ac.za/jesa/volume18/ ... dobson.pdf
model_builder
software wxmaxima
http://www.iue.tuwien.ac.at/phd/ceric/node4.html
http://www.koreascience.or.kr/article/A ... 5_v23n5_49
Numerical Models for Stress Corrosion Cracking
1. http://www.iaea.org/inis/collection/NCL ... 105093.pdf
2. http://www.gruppofrattura.it/ocs/index. ... 10442/9800
3. http://www.vtt.fi/proj/nulife/nulife_d1 ... ay2012.pdf
4. http://www.npl.co.uk/upload/pdf/stress.pdf
5. http://www.gewater.com/handbook/boiler_ ... ailure.jsp
6. Failure analysis of boiler used in thermal power plants
7. FEM model of chlorine induced failure in a boiler tube
8. https://www.escholar.manchester.ac.uk/a ... L-TEXT.PDF
9. http://lib.dr.iastate.edu/cgi/viewconte ... ntext=qnde
10.Application of perturbation methods in FEM of scc.
11. Ph D Dissertation on CZM by Nguyen O. T.
12. Ph. D. dissertation on FEM of SCC by Rimoli J.
13. shortlab and research activities
14. Modeling injected interstitial effects on void swelling in self-ion irradiation experiments -an article published using MOOSE -grime application.
15. Modeling of Corrosion Chemistry in Boiler Tubes
16. Nalco guide for BFA 2edition
17. ICASEIT2011
18. http://repository.um.edu.my/86051/1/Roo ... tation.pdf

Yours Sincerely,
Anil Kunwar
Last edited by annier on 23 Mar 2016, 11:33, edited 8 times in total.
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
annier
Posts: 1168
Joined: 27 Aug 2013, 13:51
Antispam: Yes

Re: Using multiple softwares for performing a simulation

Post by annier »

Research areas in Microelectronics by Professor Jiang Tengfei
Research areas in Physical Chemistry by Professor Susan Sinnott
Professor Sharvan K. Kumar Research Direction
http://www.brown.edu/academics/engineer ... materialia
Research in solid mechanics by Professor Allan F. Bower
Research Dimension of Professor Subodh Mhaisalkar
Computational Materials Science researches by Prof. Maryam Ghazisaeidi
Research lab of Prof. Maryam Ghazisaeidi in Computational Materials Science
Research on microstructure by Prof. Emmanuelle Marquis
Research on heat and mass transfer (in materials) by Irina Belova
Professor Han Huang's research area
http://www.gotrawama.eu/Fonderia/Struct ... Wilson.pdf
Lectures on joining and fabrication by Thomas W. Eagar
Professor Jenny Malmstrom Research Area in Nanoscience and her contributions to science
Assoc. Prof Krishnan Jayaraman and lignocellulosic composites or biocomposites
Dr. Sun Dan and her researches on Polymer based nanocomposites
Professor Lu Jiaxi and Biography
Lu Jiaxi - Journal of Cluster Science
Professor Alexandar Mihai Grumezescu and his research area
Institute for Chemical and Thermal Processing Engineering
Microstructure Science and Engineering Laboratory Pennsylvania State University
Research directions of Dr. Karthikeyan Chockalingam in PFM and tensor mechanics
1. http://www.icams.de/content/people/icam ... detail=682
2. Doctoral dissertation on homogenization theory for multiscale continuum-atomistic systems
3. 2D PFM for sintering of Ag nanoparticles
4. Crystal plasticity with JFNK
Faculty at Penn State Materials Research Institute
Phase field fracture mechanics by Miehe et al (2010)
Composite mechanics laboratory in Ghent University
Molecular Dynamics MD (Lammps) and Density Functional Theory DFT research (Quantum Espresso) of Ali Y. Nobakht
1. https://sourceforge.net/p/lammps/mailma ... &viewday=6
2. http://lammps.sandia.gov/threads/msg52735.html
Information on quantitative phase field modeling by Qi Xin-Bo

Dr. Bisesh Khanal and his research of computational modeling in Biomedicine and Bioengineering
1. github profile
2. Publications during ph d studies
3. Simul-atrophy software(finite difference method -fdm based) for computational brainimaging based on C++ src codes python scripting codes
4. Introductory literature on simul-atrophy
5. Health and medical related computational softwares developed at inria
6. Masters of Science in Computational Biology and Biomedicine

Research works of Dr. Andy Wilkins
1. ResearchGate Profile
2. Linked in Profile
3. Pawsey Supercomputing Center - Australia
4. csiro - The commonwealth scientific and industrial research organization

Dr. Tony Murphy and his Research Fields
1. Linkedin Profile
2. Research projects at CSIRO
3. Modelling of nanoscale heat transfer
4. https://www.csiro.au/

TU Delft Delft University of TechnologY
1. Department of process and energy
2. Large scale energy storage and Prof W. de Jong's Research
3. Vacancy for process and energy positions
4. Related Links

TU Graz - Graz University of Technology
1. Institute of Structural Analysis, TU Graz
2. Professor Gernot Beer and Research in Computational Structural Analysis
3. Professor Gernot Beer and people at graz university of technology
4. Research at Institute of Structural Analysis, TU Graz
5. Linked in profile of Prof Gernot Beer
6. Research gate profile of Prof Gernot Beer
7. Graz Center of Computational Engineering(GCCE)

Dalian University of Technology
1. Assoc. Prof. Wang Weiqiang and research in Biomedical Engineering
Last edited by annier on 03 May 2017, 17:35, edited 38 times in total.
Anil Kunwar
Faculty of Mechanical Engineering, Silesian University of Technology, Gliwice
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