Software Open Access

Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model

Lecrivain, Gregory


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    <subfield code="a">&lt;p&gt;Source files and selected raw data related to the manuscript &amp;quot;Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model&amp;quot; by Gregory Lecrivain, Helmholtz-Zentrum Dresden-Rossendorf, Germany, 2024.&lt;/p&gt;

&lt;p&gt;1) folder &amp;quot;manuscript&amp;quot;,&lt;br&gt;
This folder contains all text documents related to manuscript. Text and final figures are found in the directory.&lt;/p&gt;

&lt;p&gt;2) folder &amp;quot;scripts&amp;quot;&lt;br&gt;
This folder contains python and bash scripts used to post-process the raw data and prepare the figures. You will need to install some python3 libraries. Use the following command: pip install pyquaternion matplotlib scipy intersect.&lt;/p&gt;

&lt;p&gt;3) folder &amp;quot;figures&amp;quot;&lt;br&gt;
This folder contain information on how to run the simulations related to the figure. More information can be found in the README text file located in each figure/figX subfolder, where X the figure number in the manuscript.&lt;/p&gt;

&lt;p&gt;4) folder &amp;quot;src&amp;quot;&lt;br&gt;
This folder contains the all c++ files related to the source code.&lt;/p&gt;

&lt;p&gt;4.1)&lt;br&gt;
Prior to compiling, you should have gcc(7.3.0), openmpi(2.1.2), make(4.3), cmake(3.20.2), python(3.8.0), blas(3.8.0), lapack(3.8.0), boost(1.78.0), and git(2.30.1) available on your machine. The version number in the parenthesis corresponds to the one I used on the local HPC available at my institution. In my case, I type &amp;quot;module load gcc/7.3.0 openmpi/2.1.2 make/4.3 cmake/3.20.2 python/3.8.0 blas/3.8.0 lapack/3.8.0 boost/1.78.0 git/2.30.1&amp;quot;.&lt;/p&gt;

&lt;p&gt;4.2)&lt;br&gt;
To compile the libraries, open a terminal, cd to the src directory and type &amp;quot;make libs&amp;quot;. All outputs will placed in the folder $HOME/local. The libraries&amp;#39; tarballs needed to compile the code are placed in the Libs directory.&lt;/p&gt;

&lt;p&gt;4.3)&lt;br&gt;
I have manually installed paraview 5.9.1. pvpython is used to export txt data (hinge, drop and three-phase contact line) to vtk format.&lt;/p&gt;

&lt;p&gt;4.4)&lt;br&gt;
Open your ~/.bashrc file and add the following lines.&lt;br&gt;
export IGL_NUM_THREADS=1&lt;br&gt;
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/libconfig-1.7.3/lib&lt;br&gt;
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/gmp-6.2.1/lib&lt;br&gt;
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/mpfr-4.1.0/lib&lt;br&gt;
export PATH=$PATH:$HOME/microorigami/src #(or whereever, your chosen parent directory is)&lt;br&gt;
export PATH=$PATH:$HOME/microorigami/scripts #(or whereever, your chosen parent directory is)&lt;br&gt;
export PATH=$PATH:$HOME/microorigami/paraview/bin #(or whatever path you used)&lt;/p&gt;

&lt;p&gt;4.5)&lt;br&gt;
open a new terminal, cd to the src directory and type &amp;quot;make check_library_path&amp;quot;. The terminal should return&lt;br&gt;
&amp;quot;library path to libconfig is correct&amp;quot;&lt;br&gt;
&amp;quot;library path to gmp is correct&amp;quot;&lt;br&gt;
&amp;quot;library path to mpfr is correct&amp;quot;&lt;br&gt;
If that is the case, i.e. the paths are correctly set. To compile, type &amp;quot;make main post&amp;quot;. Alternatively, one can speed up the installation by typing &amp;quot;make -j 4 main post&amp;quot;, where 4 is the number of cpus I use.&lt;/p&gt;

&lt;p&gt;4.6)&lt;br&gt;
Help is available in each header file (.h) in the form of doxygen comments. Type &amp;quot;make doxy&amp;quot;. The folder html will appear under src.&lt;/p&gt;

&lt;p&gt;4.7)&lt;br&gt;
Type &amp;quot;make clean&amp;quot; to clean the src folder&lt;/p&gt;

&lt;p&gt;5) folders &amp;quot;caX_sideY_ecZ.zip&amp;quot;&lt;br&gt;
The zip files contains the raw data related to Figure 10. Here, X = 70 is the contact angle, Y = 5 the number of side panels and Z = 0.8, 1.6 and 2.4 the elasto-capillary number. After data extraction, three folders will be created, namely wd/ca70/side5/ec0.8, wd/ca70/side5/ec1.6 and wd/ca70/side5/ec2.4, where wd is your working directory. To convert the data into human-readable format (txt, vtk, stl,...) type &amp;quot;source Utils.sh; ExportScript --verbose --submit&amp;quot; in the working directory wd on the hpc. The bash function ExportScript is located in &amp;quot;scripts/Utils.sh&amp;quot;. All other raw data can be obtained by following the commands in the README text file located in each figX folder, with X=1,2,...,13. With Paraview, one is able to visualize the self-folding by loading the stl files.&lt;/p&gt;</subfield>
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