Add some recent stuff
This commit is contained in:
parent
0aa9986ada
commit
d68f8b9cd9
1
.gitignore
vendored
1
.gitignore
vendored
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*.swp
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outdir
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$pdf_mode = 1;
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$pdf_previewer = 'start evince';
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@default_files = ('tinytalk.tex');
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# Make latexmk -c remove .bbl file
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$bibtex_use = 2;
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# Make the glossaries package happy
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add_cus_dep('glo', 'gls', 0, 'run_makeglossaries');
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add_cus_dep('acn', 'acr', 0, 'run_makeglossaries');
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sub run_makeglossaries {
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my ($base_name, $path) = fileparse($_[0]);
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system("makeglossaries '$base_name'");
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}
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push @generated_exts, 'glo', 'gls', 'glg';
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push @generated_exts, 'acn', 'acr', 'alg';
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$clean_ext .= ' %R.ist %R.xdy';
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File diff suppressed because it is too large
Load Diff
@ -1,4 +0,0 @@
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* Sprache: Englisch
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* Codierung: ISO8859-1
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* Makefile existiert
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@ -1,73 +0,0 @@
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%% Encoding: ISO8859-1 %%
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% Copyright 2007 by Till Tantau
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%
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% This file may be distributed and/or modified
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%
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% 1. under the LaTeX Project Public License and/or
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% 2. under the GNU Public License.
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%
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% See the file doc/licenses/LICENSE for more details.
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%Modificated Seagull Color Theme
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%EB: official KIT colors :-)
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\definecolor{kit-green100}{rgb}{0,.59,.51}
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\definecolor{kit-green70}{rgb}{.3,.71,.65}
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\definecolor{kit-green50}{rgb}{.50,.79,.75}
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\definecolor{kit-green30}{rgb}{.69,.87,.85}
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\definecolor{kit-green15}{rgb}{.85,.93,.93}
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\definecolor{kit-blue100}{rgb}{.27,.39,.67}
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\definecolor{kit-blue70}{rgb}{.49,.57,.76}
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\definecolor{kit-blue50}{rgb}{.64,.69,.83}
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\definecolor{kit-blue30}{rgb}{.78,.82,.9}
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\definecolor{kit-blue15}{rgb}{.89,.91,.95}
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%\definecolor{kit-green100}{cmyk}{1,0,.6,0}
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%\definecolor{kit-green70}{cmyk}{.7,0,.42,0}
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%\definecolor{kit-green50}{cmyk}{.5,0,.3,0}
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%\definecolor{kit-green30}{cmyk}{.3,0,.18,0}
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%\definecolor{kit-green15}{cmyk}{.15,0,.09,0}
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\mode<presentation>
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\setbeamercolor*{normal text}{fg=black,bg=white}
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\setbeamercolor*{alerted text}{fg=red}
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\setbeamercolor*{example text}{fg=black}
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\setbeamercolor*{structure}{fg=black}
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%\setbeamerfont{alerted text}{series=\bfseries}
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\setbeamercolor*{palette primary}{fg=black,bg=black!15}
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\setbeamercolor*{palette secondary}{fg=black,bg=black!15}
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\setbeamercolor*{palette tertiary}{fg=black,bg=black!15}
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\setbeamercolor*{palette quaternary}{fg=black,bg=black!15}
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\setbeamercolor{sidebar}{bg=black!20}
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\setbeamercolor*{palette sidebar primary}{fg=black}
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\setbeamercolor*{palette sidebar secondary}{fg=black}
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\setbeamercolor*{palette sidebar tertiary}{fg=black}
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\setbeamercolor*{palette sidebar quaternary}{fg=black}
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\setbeamercolor*{item projected}{fg=black,bg=kit-green100}
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\setbeamercolor*{block title}{fg=white,bg=kit-green100}
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\setbeamercolor{block title alerted}{use=alerted text,fg=white,bg=alerted text.fg!75!black}
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\setbeamercolor*{block title example}{fg=white,bg=kit-blue100}
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\setbeamercolor*{block body}{fg=black,bg=kit-green15}
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\setbeamercolor{block body alerted}{parent=normal text,use=block title alerted,bg=block title alerted.bg!10!bg}
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\setbeamercolor*{block body example}{fg=black,bg=kit-blue15}
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\setbeamercolor*{separation line}{}
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\setbeamercolor*{fine separation line}{}
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\setbeamercolor*{background canvas}{bg=black!15}
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\setbeamercolor*{background}{bg=black!15}
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\pagecolor{black!15}
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\mode
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<all>
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@ -1,225 +0,0 @@
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%% Encoding: ISO8859-1 %%
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%% LaTeX-Beamer template for KIT design
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%% by Erik Burger, Christian Hammer
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%%
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%% modified by Christian Henrich for IKS
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%%
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%% version 1.2
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%%
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%% mostly compatible to KIT corporate design v1.2
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%% http://www.uni-karlsruhe.de/download/uka/Gestaltungsrichtlinien_komplett.pdf
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%%
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%% Problems, bugs and comments to
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%% burger@ipd.uka.de
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\usepackage[latin1]{inputenc}
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\usepackage[english,ngerman]{babel}
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\usepackage{ifthen} %For choosing the language, see below
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\usepackage{hyperref}
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\usepackage[absolute,overlay]{textpos}
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\usepackage{semirounded}
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\usepackage[abs]{overpic}
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\usepackage{times}
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\setbeamercovered{transparent}
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\useinnertheme{rounded}
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\usecolortheme{kit}
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%save space in the footer
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\beamer@compresstrue
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\newcommand{\titleimage}{IKS-beamer-motiv}
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%CH: KIT-point
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\setbeamertemplate{itemize items}{
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\begin{pgfpicture}{0mm}{0mm}{1ex}{1ex}
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{\pgfsetcornersarced{\pgfpoint{.3ex}{.3ex}}
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\pgfpathmoveto{\pgfpoint{0cm}{1ex}}
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\pgfpathlineto{\pgfpoint{1ex}{1ex}}
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\pgfpathlineto{\pgfpoint{1ex}{0cm}}}
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{\pgfsetcornersarced{\pgfpoint{.3ex}{.3ex}}
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\pgfpathmoveto{\pgfpoint{1ex}{0cm}}
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\pgfpathlineto{\pgfpointorigin}
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\pgfpathlineto{\pgfpoint{0cm}{1ex}}}
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\color{kit-green100}
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\pgfusepath{fill}
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\end{pgfpicture}%
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}
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\setbeamertemplate{title page}
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{
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\thispagestyle{empty}
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%middle block with name of institute
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\begin{textblock*}{\paperwidth}(1mm,42.25mm)
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\begin{pgfpicture}{0mm}{0mm}{\paperwidth-2mm}{6mm}
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\color{black!50}
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\pgfpathrectangle{\pgfpoint{0mm}{0mm}}{\pgfpoint{\paperwidth-2mm}{6mm}}
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\pgfusepath{fill}
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\pgftext[at=\pgfpoint{8.5mm}{3mm},left,center]{\textcolor{white}{\tiny\textsc{\insertinstitute}}}
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\end{pgfpicture}
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\end{textblock*}
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%elements on title page
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%KIT logo
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\begin{textblock*}{16mm}(4mm,4mm)
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\iflanguage{english}{
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\includegraphics[width=15mm]{logos/kitlogo_rgb}
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}{
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\includegraphics[width=15mm]{logos/kit_logo_de_4c_positiv}
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}
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\end{textblock*}
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%title
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\begin{textblock*}{120mm}(9.5mm,16mm)
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\begin{beamercolorbox}[wd=118mm,ht=14mm,dp=3mm,left]{white}%
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\LARGE\textbf{\inserttitle}
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\end{beamercolorbox}
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\end{textblock*}
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%subtitle
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\begin{textblock*}{120mm}(9.5mm,33mm)
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\tiny \insertsubtitle
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\end{textblock*}
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%author
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\begin{textblock*}{120mm}(9.5mm,36mm)
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\tiny\insertauthor%~\textbar~\insertshortdate
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\end{textblock*}
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%Universit<69>t Karlsruhe logo
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%\begin{textblock*}{23mm}(106mm,89.6mm)
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%\iflanguage{english}{
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%\includegraphics[width=20mm]{logos/uka_wortbild_en}
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%}{
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%\includegraphics[width=20mm]{logos/uka_wortbild_de}
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%}
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%\end{textblock*}
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%Forschungszentrum Karlsruhe logo
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%\begin{textblock*}{21mm}(81mm,89.6mm)
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%\includegraphics[width=20mm]{logos/fzk_wortbild}
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%\end{textblock*}
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%legal KIT text
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\begin{textblock*}{80mm}[0,1](4mm,94mm)
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\fontsize{4pt}{6pt}\selectfont
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\iflanguage{english}{
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KIT -- The Research University in the Helmholtz Association}
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{KIT -- Die Forschungsuniversit{\"a}t in der Helmholtz-Gemeinschaft}
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\end{textblock*}
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\begin{textblock*}{20mm}[0,1](110mm,92mm)
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\fontsize{8pt}{8pt}\selectfont
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\bfseries
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\textcolor{black!75}{
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\href{http://www.kit.edu}{www.kit.edu}
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}
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\end{textblock*}
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% title image
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\begin{textblock*}{\paperwidth}(1mm,48.5mm)
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\begin{overpic}[width=158mm,height=40mm]{logos/\titleimage}
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\put(-6,-3){
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%mask curve for lower left corner of title image
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\begin{pgfpicture}{0mm}{0mm}{3mm}{3mm}
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\pgfpathqmoveto{0mm}{0mm}
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\pgfpathlineto{\pgfpoint{3mm}{0mm}}
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\pgfpathlineto{\pgfpoint{3mm}{1mm}}
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{\pgfsetcornersarced{\pgfpoint{2mm}{2mm}}
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\pgfpathlineto{\pgfpoint{1mm}{1mm}}
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\pgfpathlineto{\pgfpoint{1mm}{3mm}}}
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\pgfpathmoveto{\pgfpoint{1mm}{3mm}}
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\pgfpathlineto{\pgfpoint{0mm}{3mm}}
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\pgfpathlineto{\pgfpoint{0mm}{0mm}}
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\pgfpathclose
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\color{black!15}
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\pgfusepath{fill}
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\end{pgfpicture}
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}
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\end{overpic}
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\end{textblock*}
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}
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%background for pages
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%CH: for plain frames
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\newlength{\kitbottom}
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\usebackgroundtemplate{
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\setlength{\kitbottom}{\ifbeamer@plainframe1mm\else9mm\fi}%
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\begin{pgfpicture}{0mm}{0mm}{\paperwidth}{\paperheight}
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||||
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{\pgfsetcornersarced{\pgfpoint{2mm}{2mm}}
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\pgfpathmoveto{\pgfpoint{\paperwidth-1mm}{\kitbottom}}
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\pgfpathlineto{\pgfpoint{1mm}{\kitbottom}}
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\pgfpathlineto{\pgfpoint{1mm}{\paperheight-1mm}}}
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{\pgfsetcornersarced{\pgfpoint{2mm}{2mm}}
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\pgfpathmoveto{\pgfpoint{1mm}{\paperheight-1mm}}
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\pgfpathlineto{\pgfpoint{\paperwidth-1mm}{\paperheight-1mm}}
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\pgfpathlineto{\pgfpoint{\paperwidth-1mm}{\kitbottom}}}
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\color{white}
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\pgfusepath{fill}
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\end{pgfpicture}%
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}
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%frametitle
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\setbeamertemplate{frametitle}
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{
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\vspace{2mm} \hspace*{-4mm}
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\vbox{\hsize=9cm\bfseries\insertframetitle}
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\begin{textblock*}{15mm}(140mm,4mm)
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\iflanguage{english}{
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\includegraphics[width=14mm]{logos/kitlogo_rgb}
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}{
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\includegraphics[width=14mm]{logos/kit_logo_de_4c_positiv}
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}
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\end{textblock*}
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\begin{textblock*}{1.5mm}(1mm,1mm)
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\begin{pgfpicture}{0mm}{0mm}{1.5mm}{9mm}
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\color{kit-green100}
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\pgfpathrectangle{\pgfpoint{0mm}{0mm}}{\pgfpoint{1.5mm}{9mm}}
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\pgfusepath{fill}
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\end{pgfpicture}%
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\end{textblock*}
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}
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\setbeamertemplate{headline}
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{
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}
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%footer
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\setbeamertemplate{footline}
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{
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\vskip.4mm
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\begin{beamercolorbox}[ht=2.4mm, dp=3mm]{section in head/foot}
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%include mini frame navigation
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\insertnavigation{\paperwidth}
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\end{beamercolorbox}
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\begin{beamercolorbox}[wd=0.7\textwidth,ht=2.2mm,dp=1.5mm,leftskip=1.3em,rightskip=.5em]{author in head/foot}%
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\usebeamerfont{author in head/foot}%
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\insertshortauthor\hspace{2.5pt}--\hspace{2.5pt}\insertshorttitle
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\end{beamercolorbox}%
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\vspace*{-4mm}\hspace*{0.7\textwidth}%
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\begin{beamercolorbox}[wd=0.3\textwidth,ht=2.2mm,dp=1.5mm,left,leftskip=.5em]{title in head/foot}%
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\usebeamerfont{title in head/foot}%
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\hfill\hspace{65pt}\insertframenumber{}/\inserttotalframenumber
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% vorher: \hfill\insertshortdate\hspace{30pt}\insertframenumber{}/\inserttotalframenumber
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\end{beamercolorbox}%
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}
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%%EOF
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Binary file not shown.
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Before Width: | Height: | Size: 1.3 MiB |
Binary file not shown.
Binary file not shown.
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Before Width: | Height: | Size: 86 KiB |
@ -1,19 +0,0 @@
|
||||
@article{dh76,
|
||||
title={{New Directions in Cryptography}},
|
||||
author={Whitfield Diffie and Martin Hellman},
|
||||
journal={IEEE Transactions on Information Theory},
|
||||
volume={22},
|
||||
number={6},
|
||||
pages={644--654},
|
||||
year={1976}
|
||||
}
|
||||
|
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@book{kl07,
|
||||
author = {Katz, Jonathan and Lindell, Yehuda},
|
||||
title = {Introduction to Modern Cryptography (Chapman \& Hall/Crc Cryptography and Network Security Series)},
|
||||
year = {2007},
|
||||
isbn = {1584885513},
|
||||
publisher = {Chapman \& Hall/CRC},
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}
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%\pgfpathcurveto%
|
||||
%{\pgfpoint{\the\bmb@dima}{-3bp}}%
|
||||
%{\pgfpoint{\the\bmb@dimb}{-1.2bp}}%
|
||||
%{\pgfpoint{\the\bmb@dimb}{1bp}}%
|
||||
{
|
||||
\bmb@dima=\ht\bmb@box%
|
||||
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
|
||||
\pgfpathlineto{\pgfpoint{-4bp}{\bmb@dima}}
|
||||
\pgfusepath{fill}
|
||||
}
|
||||
\ifbmb@shadow%
|
||||
{
|
||||
\color{black!50!bg}
|
||||
\pgfsetlinewidth{0pt}
|
||||
\pgfpathmoveto{\pgfpoint{\bmb@dimb}{-.5bp}}
|
||||
\bmb@dima=\ht\bmb@box%
|
||||
\advance\bmb@dima by\bmb@prevheight%
|
||||
\advance\bmb@dima by 1bp%
|
||||
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
|
||||
\pgfusepath{stroke}
|
||||
\bmb@temp=\bmb@dima
|
||||
\advance\bmb@dima by 1bp%
|
||||
\color{black!31!bg}
|
||||
\pgfpathmoveto{\pgfpoint{\bmb@dimb}{\bmb@temp}}
|
||||
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
|
||||
\pgfusepath{stroke}
|
||||
\advance\bmb@dima by 1bp%
|
||||
\advance\bmb@temp by 1bp%
|
||||
\color{black!19!bg}
|
||||
\pgfpathmoveto{\pgfpoint{\bmb@dimb}{\bmb@temp}}
|
||||
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
|
||||
\pgfusepath{stroke}
|
||||
\advance\bmb@dima by 1bp%
|
||||
\advance\bmb@temp by 1bp%
|
||||
\color{black!6!bg}
|
||||
\pgfpathmoveto{\pgfpoint{\bmb@dimb}{\bmb@temp}}
|
||||
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
|
||||
\pgfusepath{stroke}
|
||||
\advance\bmb@dima by 1.5bp%
|
||||
\advance\bmb@temp by 1bp%
|
||||
\color{bg}
|
||||
\pgfpathmoveto{\pgfpoint{\bmb@dimb}{\bmb@temp}}
|
||||
\pgfpathlineto{\pgfpoint{\bmb@dimb}{\bmb@dima}}
|
||||
\pgfusepath{stroke}
|
||||
}
|
||||
\fi
|
||||
\end{pgfpicture}%
|
||||
\box\bmb@box%
|
||||
}%
|
||||
\ifbmb@shadow%
|
||||
\vskip4bp minus 2bp%
|
||||
\else%
|
||||
\vskip2bp%
|
||||
\fi%
|
||||
\egroup% of \vbox\bgroup
|
||||
}
|
||||
|
||||
Binary file not shown.
@ -1,83 +0,0 @@
|
||||
%% Encoding: ISO8859-1 %%
|
||||
|
||||
%% LaTeX-Beamer template for KIT design
|
||||
%% by Erik Burger, Christian Hammer
|
||||
%%
|
||||
%% modified by Christian Henrich and Matthias Gabel for IKS/ITI
|
||||
%%
|
||||
%% version 1.3
|
||||
%%
|
||||
%% mostly compatible to KIT corporate design v1.2
|
||||
%% http://www.uni-karlsruhe.de/download/uka/Gestaltungsrichtlinien_komplett.pdf
|
||||
|
||||
\documentclass[18pt,aspectratio=169]{beamer}
|
||||
\usetheme{kit}
|
||||
|
||||
\usepackage{comment}
|
||||
\usepackage{pdfpages}
|
||||
|
||||
% if a custom picture is to be used on the title page, copy it into the 'logos'
|
||||
% directory, in the line below, replace 'mypicture' with the
|
||||
% filename (without extension) and uncomment the line
|
||||
|
||||
\renewcommand{\titleimage}{collagen}
|
||||
|
||||
% (picture proportions: 63 : 20, *.eps format if you use latex+dvips+ps2pdf,
|
||||
% *.jpg/*.png/*.pdf if you use pdflatex)
|
||||
|
||||
% if you want to see BibTeX keys in the references view instead of the symbol,
|
||||
% uncomment the following line
|
||||
% \usebibitemtemplate{\insertbiblabel}
|
||||
|
||||
% uncomment the following line if you want to hide the navigation symbols
|
||||
%\beamertemplatenavigationsymbolsempty
|
||||
|
||||
% the presentation starts here
|
||||
|
||||
\title[An ECM Model for Cells In Silico]{An ECM Model for Cells in Silico}
|
||||
% \subtitle{}
|
||||
\author{Paul Brinkmeier}
|
||||
|
||||
\institute[SCC]{Steinbuch Centre for Computing} % Deutsch
|
||||
%\institute[ITI]{Department of Informatics, Institute of Theoretical Informatics} % Englisch
|
||||
|
||||
\begin{document}
|
||||
|
||||
\selectlanguage{english} % Deutsch
|
||||
% \selectlanguage{ngerman} % Englisch
|
||||
%title page
|
||||
\begin{frame}
|
||||
\titlepage{}
|
||||
\end{frame}
|
||||
|
||||
\include{vortrag}
|
||||
|
||||
\begin{comment}
|
||||
\section{References}
|
||||
\begin{frame}
|
||||
\frametitle{References}
|
||||
\bibliography{references}
|
||||
\bibliographystyle{plain} %does not render "url" fields...
|
||||
% \bibliographystyle{IEEEtran} %does render "url" fields, requires "_"s and "#"s to be escaped, e.g. "\_".
|
||||
\end{frame}
|
||||
\end{comment}
|
||||
|
||||
\section{End}
|
||||
\begin{frame}
|
||||
\begin{columns}
|
||||
\column{0.45\textwidth}
|
||||
\includegraphics[page=2,width=0.9\textwidth]{tinytalk2}
|
||||
\column{0.45\textwidth}
|
||||
\includegraphics[page=3,width=0.9\textwidth]{tinytalk2}
|
||||
\end{columns}
|
||||
\vfill
|
||||
\begin{columns}
|
||||
\column{0.45\textwidth}
|
||||
\includegraphics[page=7,width=0.9\textwidth]{tinytalk2}
|
||||
\column{0.45\textwidth}
|
||||
\includegraphics[page=8,width=0.9\textwidth]{tinytalk2}
|
||||
\end{columns}
|
||||
\end{frame}
|
||||
|
||||
\end{document}
|
||||
|
||||
Binary file not shown.
@ -1,167 +0,0 @@
|
||||
\section{Intro}
|
||||
|
||||
\begin{frame}{NAStJA: An MPI Stencil Code Solver}
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.8\textwidth]{nastja.png}
|
||||
\end{figure}
|
||||
|
||||
\begin{itemize}
|
||||
\item CiS uses NAStJA under the hood
|
||||
\item NAStJA is a massively parallel stencil code solver \\
|
||||
$\implies$ CiS extensions should be stencils
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\begin{frame}{ECM Viscoelasticity:\\A Factor in Cell Behavior}
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.48\textwidth]{ecm-cells.png}
|
||||
\end{figure}
|
||||
|
||||
\begin{itemize}
|
||||
\item Collagen networks in the ECM mechanically restrict cells
|
||||
\item Collagen networks are \emph{viscoelastic}
|
||||
\item ECM viscoelasticity influences cell behavior
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\section{ECM Model}
|
||||
|
||||
\begin{frame}{Modeling ECM Mechanics in CiS}
|
||||
How can we model ECM mechanics in CiS?
|
||||
|
||||
\vfill{}
|
||||
|
||||
Two main requirements:
|
||||
|
||||
\begin{itemize}
|
||||
\item Model exhibits viscoelastic properties
|
||||
\item Model can be implemented as a stencil in NAStJA
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\begin{frame}{ECM Models in Literature}
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.64\textwidth]{models.png}
|
||||
\end{figure}
|
||||
|
||||
\begin{itemize}
|
||||
\item A host of different ECM models exist
|
||||
\item Various foci, e.g. mechanics, growth factors
|
||||
\item Various approaches, e.g. FEM, Molecular Dynamics
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\begin{frame}{My Approach}
|
||||
Two main requirements:
|
||||
|
||||
\begin{itemize}
|
||||
\item Model exhibits viscoelastic properties
|
||||
\item Model can be implemented as a stencil in NAStJA
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\section{Methods}
|
||||
|
||||
\begin{frame}{Lattice Boltzmann Method}
|
||||
\begin{figure}
|
||||
\includegraphics[width=0.6\textwidth]{lbm.png}
|
||||
\end{figure}
|
||||
|
||||
\[
|
||||
f_i(\mathbf{x} + \mathbf{c}_i, t + 1) = f_i(\mathbf{x}, t) - \frac{1}{\tau} (f_i(\mathbf{x}, t) - f_i^\text{eq}(\mathbf{x}, t))
|
||||
\]
|
||||
|
||||
\begin{itemize}
|
||||
\item Discretized particle velocities per lattice site
|
||||
\item Update Step: Streaming + Collision
|
||||
\item Usually used for hydrodynamics
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\begin{frame}{Elastic Lattice Model}
|
||||
\begin{columns}
|
||||
\column{0.35\textwidth}
|
||||
\begin{figure}
|
||||
\includegraphics[width=\textwidth]{elm.png}
|
||||
\end{figure}
|
||||
|
||||
\column{0.65\textwidth}
|
||||
\[
|
||||
\mathbf{F}_{ij} = \mathbf{r}_{ij} K_{ij} (\mathbf{u}_{ij} \cdot \mathbf{x}_{ij}) + \frac{c \mathbf{u}_{ij}}{|\mathbf{x}_{ij}|^2} + \eta \mathbf{v}_{ij}
|
||||
\]
|
||||
|
||||
\begin{itemize}
|
||||
\item A square lattice based discrete particle method
|
||||
\item Each lattice site represents a particle
|
||||
\item Particles are connected to neighbors by springs
|
||||
\end{itemize}
|
||||
\end{columns}
|
||||
\end{frame}
|
||||
|
||||
\begin{frame}{My Approach}
|
||||
Two main requirements:
|
||||
|
||||
\begin{itemize}
|
||||
\item Model exhibits viscoelastic properties \checkmark{}
|
||||
\item Model can be implemented as a stencil in NAStJA \checkmark{}
|
||||
\end{itemize}
|
||||
|
||||
\vfill
|
||||
|
||||
Challenges:
|
||||
|
||||
\begin{itemize}
|
||||
\item How do we integrate the model with the CPM?
|
||||
\item How can it be implemented in NAStJA?
|
||||
\item How do we make it fast?
|
||||
\end{itemize}
|
||||
\end{frame}
|
||||
|
||||
\begin{comment}
|
||||
\section{Intro}
|
||||
\subsection{Subsection 1.1}
|
||||
\frame{
|
||||
\frametitle{Example slide A}
|
||||
\begin{itemize}
|
||||
\item PCM, Citation: \cite{dh76,kl07} %\language
|
||||
\pause
|
||||
\item Bullet point 2
|
||||
\item \dots
|
||||
\end{itemize}
|
||||
}
|
||||
\subsection{Subsection 1.2}
|
||||
\frame{
|
||||
\frametitle{Example slide B}
|
||||
\begin{block}{Block 1}
|
||||
\begin{itemize}
|
||||
\item Test: ÄÖÜäöüß
|
||||
\pause
|
||||
\item Bullet point 2
|
||||
\item \dots
|
||||
\end{itemize}
|
||||
\end{block}
|
||||
}
|
||||
\section{Section 2}
|
||||
\frame{
|
||||
\frametitle{Example slide C}
|
||||
\begin{exampleblock}{Example 1}
|
||||
\begin{itemize}
|
||||
\item Bullet point 1
|
||||
\pause
|
||||
\item Bullet point 2
|
||||
\item \dots
|
||||
\end{itemize}
|
||||
\end{exampleblock}
|
||||
}
|
||||
\frame{
|
||||
\frametitle{Example slide D}
|
||||
\begin{alertblock}{Alert 1}
|
||||
\begin{itemize}
|
||||
\item Bullet point 1
|
||||
\pause
|
||||
\item Bullet point 2
|
||||
\item \dots
|
||||
\end{itemize}
|
||||
\end{alertblock}
|
||||
}
|
||||
\end{comment}
|
||||
File diff suppressed because one or more lines are too long
@ -248,7 +248,7 @@
|
||||
"name": "python",
|
||||
"nbconvert_exporter": "python",
|
||||
"pygments_lexer": "ipython3",
|
||||
"version": "3.9.13"
|
||||
"version": "3.10.11"
|
||||
}
|
||||
},
|
||||
"nbformat": 4,
|
||||
|
||||
2389
experiments/Zener.jl
Normal file
2389
experiments/Zener.jl
Normal file
File diff suppressed because it is too large
Load Diff
BIN
experiments/__pycache__/collatz.cpython-310.pyc
Normal file
BIN
experiments/__pycache__/collatz.cpython-310.pyc
Normal file
Binary file not shown.
31
experiments/collatz.py
Normal file
31
experiments/collatz.py
Normal file
@ -0,0 +1,31 @@
|
||||
import time
|
||||
|
||||
def collatz(x):
|
||||
seq = [x]
|
||||
while x != 1:
|
||||
if x % 2 == 0:
|
||||
x //= 2
|
||||
else:
|
||||
x = 3 * x + 1
|
||||
seq.append(x)
|
||||
return seq
|
||||
|
||||
if __name__ == "__main__":
|
||||
best = None
|
||||
try:
|
||||
i = 1
|
||||
start = time.time()
|
||||
while True:
|
||||
pair = (i, collatz(i))
|
||||
|
||||
if (not best or len(pair[1]) > len(best[1])) and not any(c >= 2**31 for c in pair[1]):
|
||||
best = pair
|
||||
|
||||
if i % 10000 == 0:
|
||||
now = time.time()
|
||||
print(f"{i:>10} best: {best[0]:>10} {len(best[1]):>5} {(now - start) * 1000 / i:5.2}ns/seq")
|
||||
i += 1
|
||||
except KeyboardInterrupt:
|
||||
pass
|
||||
|
||||
print(best)
|
||||
96
experiments/configs/genesis.json
Normal file
96
experiments/configs/genesis.json
Normal file
@ -0,0 +1,96 @@
|
||||
{
|
||||
"#Testing": {
|
||||
"description": "Cellular Potts Model with dynamic ECM"
|
||||
},
|
||||
"Application": "Cells",
|
||||
"Geometry": {
|
||||
"blocksize": [80, 40, 20],
|
||||
"blockcount": [1, 2, 4]
|
||||
},
|
||||
"Settings": {
|
||||
"timesteps": 100,
|
||||
"randomseed": 42
|
||||
},
|
||||
"Filling": {
|
||||
"cells": [
|
||||
{
|
||||
"shape": "cube",
|
||||
"box": [
|
||||
[21, 35, 10],
|
||||
[25, 39, 15]
|
||||
],
|
||||
"celltype": 0
|
||||
},
|
||||
{
|
||||
"shape": "cube",
|
||||
"box": [
|
||||
[15, 15, 14],
|
||||
[22, 22, 20]
|
||||
],
|
||||
"celltype": 0
|
||||
}
|
||||
]
|
||||
},
|
||||
"CellsInSilico": {
|
||||
"adhesion": {
|
||||
"matrix": [
|
||||
[0, 0, 0, 0],
|
||||
[0, 20, 5, 5],
|
||||
[0, 5, 10, 5],
|
||||
[0, 5, 5, 5]
|
||||
]
|
||||
},
|
||||
"potential": {
|
||||
"direction": [1, 1, 0],
|
||||
"coupling": [0, 150, 100, 50]
|
||||
},
|
||||
"temperature": 15,
|
||||
"volume": {
|
||||
"default": {
|
||||
"storage": "const",
|
||||
"value": 300
|
||||
},
|
||||
"lambda": {
|
||||
"storage": "const",
|
||||
"value": 10
|
||||
}
|
||||
},
|
||||
"surface": {
|
||||
"default": {
|
||||
"storage": "const",
|
||||
"value": 400
|
||||
},
|
||||
"lambda": {
|
||||
"storage": "const",
|
||||
"value": 10
|
||||
}
|
||||
},
|
||||
"cleaner": {
|
||||
"killdistance": 100
|
||||
},
|
||||
"checkerboard": "00",
|
||||
"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
|
||||
"centerofmass": {
|
||||
"steps": 10
|
||||
},
|
||||
"dynamicecm": {
|
||||
"enabled": true,
|
||||
"deltat": 0.1
|
||||
}
|
||||
},
|
||||
"Writers": {
|
||||
"ParallelVTK_Cells": {
|
||||
"writer": "ParallelVtkImage",
|
||||
"outputtype": "UInt32",
|
||||
"field": "cells",
|
||||
"steps": 5
|
||||
},
|
||||
"ParallelVTK_Displacement": {
|
||||
"writer": "ParallelVtkImage",
|
||||
"outputtype": "Float32",
|
||||
"field": "dynamicecm_displacement",
|
||||
"steps": 1
|
||||
}
|
||||
},
|
||||
"WriteActions": ["ParallelVTK_Cells", "ParallelVTK_Displacement"]
|
||||
}
|
||||
75
experiments/configs/small.json
Normal file
75
experiments/configs/small.json
Normal file
@ -0,0 +1,75 @@
|
||||
{
|
||||
"#Testing": {
|
||||
"description": "Cellular Potts Model with dynamic ECM"
|
||||
},
|
||||
"Application": "Cells",
|
||||
"Geometry": {
|
||||
"blocksize": [15, 15, 15],
|
||||
"blockcount": [1, 1, 1]
|
||||
},
|
||||
"Settings": {
|
||||
"timesteps": 100,
|
||||
"randomseed": 42
|
||||
},
|
||||
"Filling": {
|
||||
"cells": [
|
||||
]
|
||||
},
|
||||
"CellsInSilico": {
|
||||
"adhesion": {
|
||||
"matrix": [
|
||||
[0, 0, 0, 0],
|
||||
[0, 20, 5, 5],
|
||||
[0, 5, 10, 5],
|
||||
[0, 5, 5, 5]
|
||||
]
|
||||
},
|
||||
"temperature": 15,
|
||||
"volume": {
|
||||
"default": {
|
||||
"storage": "const",
|
||||
"value": 300
|
||||
},
|
||||
"lambda": {
|
||||
"storage": "const",
|
||||
"value": 10
|
||||
}
|
||||
},
|
||||
"potential": {
|
||||
"direction": [1, 1, 0],
|
||||
"coupling": [0, 150, 100, 50]
|
||||
},
|
||||
"surface": {
|
||||
"default": {
|
||||
"storage": "const",
|
||||
"value": 400
|
||||
},
|
||||
"lambda": {
|
||||
"storage": "const",
|
||||
"value": 10
|
||||
}
|
||||
},
|
||||
"cleaner": {
|
||||
"killdistance": 100
|
||||
},
|
||||
"checkerboard": "00",
|
||||
"energyfunctions": ["Volume00", "Surface00", "Adhesion00", "Potential00"],
|
||||
"centerofmass": {
|
||||
"steps": 10
|
||||
},
|
||||
"dynamicecm": {
|
||||
"enabled": true,
|
||||
"deltat": 0.1,
|
||||
"eta": 0.5
|
||||
}
|
||||
},
|
||||
"Writers": {
|
||||
"ParallelVTK_Displacement": {
|
||||
"writer": "ParallelVtkImage",
|
||||
"outputtype": "Float32",
|
||||
"field": "dynamicecm_displacement",
|
||||
"steps": 1
|
||||
}
|
||||
},
|
||||
"WriteActions": ["ParallelVTK_Displacement"]
|
||||
}
|
||||
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Reference in New Issue
Block a user