June 28, 2024 Software Open Access

Lecrivain, Gregory

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{
  "title": "Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model", 
  "id": "3033", 
  "issued": {
    "date-parts": [
      [
        2024, 
        6, 
        28
      ]
    ]
  }, 
  "abstract": "<p>Source files and selected raw data related to the manuscript &quot;Self-folding of two-dimensional thin templates into pyramidal micro-structures by a liquid drop - a numerical model&quot; by Gregory Lecrivain, Helmholtz-Zentrum Dresden-Rossendorf, Germany, 2024.</p>\n\n<p>1) folder &quot;manuscript&quot;,<br>\nThis folder contains all text documents related to manuscript. Text and final figures are found in the directory.</p>\n\n<p>2) folder &quot;scripts&quot;<br>\nThis 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.</p>\n\n<p>3) folder &quot;figures&quot;<br>\nThis 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.</p>\n\n<p>4) folder &quot;src&quot;<br>\nThis folder contains the all c++ files related to the source code.</p>\n\n<p>4.1)<br>\nPrior 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 &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&quot;.</p>\n\n<p>4.2)<br>\nTo compile the libraries, open a terminal, cd to the src directory and type &quot;make libs&quot;. All outputs will placed in the folder $HOME/local. The libraries&#39; tarballs needed to compile the code are placed in the Libs directory.</p>\n\n<p>4.3)<br>\nI have manually installed paraview 5.9.1. pvpython is used to export txt data (hinge, drop and three-phase contact line) to vtk format.</p>\n\n<p>4.4)<br>\nOpen your ~/.bashrc file and add the following lines.<br>\nexport IGL_NUM_THREADS=1<br>\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/libconfig-1.7.3/lib<br>\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/gmp-6.2.1/lib<br>\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/local/mpfr-4.1.0/lib<br>\nexport PATH=$PATH:$HOME/microorigami/src #(or whereever, your chosen parent directory is)<br>\nexport PATH=$PATH:$HOME/microorigami/scripts #(or whereever, your chosen parent directory is)<br>\nexport PATH=$PATH:$HOME/microorigami/paraview/bin #(or whatever path you used)</p>\n\n<p>4.5)<br>\nopen a new terminal, cd to the src directory and type &quot;make check_library_path&quot;. The terminal should return<br>\n&quot;library path to libconfig is correct&quot;<br>\n&quot;library path to gmp is correct&quot;<br>\n&quot;library path to mpfr is correct&quot;<br>\nIf that is the case, i.e. the paths are correctly set. To compile, type &quot;make main post&quot;. Alternatively, one can speed up the installation by typing &quot;make -j 4 main post&quot;, where 4 is the number of cpus I use.</p>\n\n<p>4.6)<br>\nHelp is available in each header file (.h) in the form of doxygen comments. Type &quot;make doxy&quot;. The folder html will appear under src.</p>\n\n<p>4.7)<br>\nType &quot;make clean&quot; to clean the src folder</p>\n\n<p>5) folders &quot;caX_sideY_ecZ.zip&quot;<br>\nThe 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 &quot;source Utils.sh; ExportScript --verbose --submit&quot; in the working directory wd on the hpc. The bash function ExportScript is located in &quot;scripts/Utils.sh&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.</p>", 
  "version": "1.1", 
  "DOI": "10.14278/rodare.3033", 
  "type": "article", 
  "author": [
    {
      "family": "Lecrivain, Gregory"
    }
  ], 
  "publisher": "Rodare", 
  "language": "eng"
}